--- /dev/null
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read Genbank entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'biopieces'
+require 'genbank'
+
+casts = []
+casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'num', :short=>'n', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'keys', :short=>'k', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'features', :short=>'f', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'qualifiers', :short=>'q', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+hash_keys = options[:keys].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:keys]
+hash_feats = options[:features].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:features]
+hash_quals = options[:qualifiers].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:qualifiers]
+
+bp.each_record do |record|
+ bp.puts record
+end
+
+num = 0
+last = false
+
+if options.has_key? :data_in
+ options[:data_in].each do |file|
+ Genbank.open(file, mode='r') do |gb|
+ gb.each(hash_keys, hash_feats, hash_quals) do |entry|
+ bp.puts entry
+
+ num += 1
+
+ if options.has_key? :num and options[:num] == num
+ last = true
+ break
+ end
+ end
+ end
+
+ break if last
+ end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
--- /dev/null
+LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p
+ (AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION U49845
+VERSION U49845.1 GI:1293613
+KEYWORDS .
+SOURCE Saccharomyces cerevisiae (baker's yeast)
+ ORGANISM Saccharomyces cerevisiae
+ Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
+ Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE 1 (bases 1 to 5028)
+ AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.
+ TITLE Cloning and sequence of REV7, a gene whose function is required for
+ DNA damage-induced mutagenesis in Saccharomyces cerevisiae
+ JOURNAL Yeast 10 (11), 1503-1509 (1994)
+ PUBMED 7871890
+REFERENCE 2 (bases 1 to 5028)
+ AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M.
+ TITLE Selection of axial growth sites in yeast requires Axl2p, a novel
+ plasma membrane glycoprotein
+ JOURNAL Genes Dev. 10 (7), 777-793 (1996)
+ PUBMED 8846915
+REFERENCE 3 (bases 1 to 5028)
+ AUTHORS Roemer,T.
+ TITLE Direct Submission
+ JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New
+ Haven, CT, USA
+FEATURES Location/Qualifiers
+ source 1..5028
+ /organism="Saccharomyces cerevisiae"
+ /db_xref="taxon:4932"
+ /chromosome="IX"
+ /map="9"
+ CDS <1..206
+ /codon_start=3
+ /product="TCP1-beta"
+ /protein_id="AAA98665.1"
+ /db_xref="GI:1293614"
+ /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
+ AEVLLRVDNIIRARPRTANRQHM"
+ gene 687..3158
+ /gene="AXL2"
+ CDS 687..3158
+ /gene="AXL2"
+ /note="plasma membrane glycoprotein"
+ /codon_start=1
+ /function="required for axial budding pattern of S.
+ cerevisiae"
+ /product="Axl2p"
+ /protein_id="AAA98666.1"
+ /db_xref="GI:1293615"
+ /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF
+ TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN
+ VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE
+ VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE
+ TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV
+ YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG
+ DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ
+ DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA
+ NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA
+ CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN
+ NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ
+ SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS
+ YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK
+ HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL
+ VDFSNKSNVNVGQVKDIHGRIPEML"
+ gene complement(3300..4037)
+ /gene="REV7"
+ CDS complement(3300..4037)
+ /gene="REV7"
+ /codon_start=1
+ /product="Rev7p"
+ /protein_id="AAA98667.1"
+ /db_xref="GI:1293616"
+ /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ
+ FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD
+ KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR
+ RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK
+ LISGDDKILNGVYSQYEEGESIFGSLF"
+ORIGIN
+ 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
+ 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
+ 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
+ 181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg
+ 241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa
+ 301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa
+ 361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat
+ 421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga
+ 481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc
+ 541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga
+ 601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta
+ 661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag
+ 721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa
+ 781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata
+ 841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga
+ 901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac
+ 961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg
+ 1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc
+ 1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa
+ 1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca
+ 1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac
+ 1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa
+ 1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag
+ 1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct
+ 1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac
+ 1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa
+ 1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc
+ 1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata
+ 1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca
+ 1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc
+ 1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc
+ 1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca
+ 1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc
+ 1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg
+ 2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt
+ 2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc
+ 2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg
+ 2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca
+ 2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata
+ 2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg
+ 2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga
+ 2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt
+ 2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat
+ 2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt
+ 2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc
+ 2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag
+ 2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta
+ 2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa
+ 2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact
+ 2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt
+ 3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa
+ 3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag
+ 3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct
+ 3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt
+ 3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact
+ 3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa
+ 3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg
+ 3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt
+ 3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc
+ 3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca
+ 3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc
+ 3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc
+ 3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat
+ 3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa
+ 3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga
+ 3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat
+ 3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc
+ 4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc
+ 4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa
+ 4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg
+ 4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc
+ 4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt
+ 4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg
+ 4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg
+ 4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt
+ 4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt
+ 4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat
+ 4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc
+ 4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct
+ 4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta
+ 4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac
+ 4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct
+ 4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct
+ 4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc
+//
--- /dev/null
+ORGANISM: Saccharomyces cerevisiaeEukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+DB_XREF: taxon:4932
+CHROMOSOME: IX
+MAP: 9
+FEATURE: source
+LOCATOR: 1..5028
+LOCUS: SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION: Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p(AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION: U49845
+VERSION: U49845.1 GI:1293613
+KEYWORDS: .
+SOURCE: Saccharomyces cerevisiae (baker's yeast)
+REFERENCE: 1 (bases 1 to 5028);2 (bases 1 to 5028);3 (bases 1 to 5028)
+AUTHORS: Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.;Roemer,T., Madden,K., Chang,J. and Snyder,M.;Roemer,T.
+TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA damage-induced mutagenesis in Saccharomyces cerevisiae;Selection of axial growth sites in yeast requires Axl2p, a novelplasma membrane glycoprotein;Direct Submission
+JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA
+PUBMED: 7871890;8846915
+SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgat
+---
+PRODUCT: TCP1-beta
+PROTEIN_ID: AAA98665.1
+DB_XREF: GI:1293614
+TRANSLATION: SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM
+FEATURE: CDS
+LOCATOR: <1..206
+LOCUS: SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION: Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p(AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION: U49845
+VERSION: U49845.1 GI:1293613
+KEYWORDS: .
+SOURCE: Saccharomyces cerevisiae (baker's yeast)
+ORGANISM: Saccharomyces cerevisiaeEukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE: 1 (bases 1 to 5028);2 (bases 1 to 5028);3 (bases 1 to 5028)
+AUTHORS: Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.;Roemer,T., Madden,K., Chang,J. and Snyder,M.;Roemer,T.
+TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA damage-induced mutagenesis in Saccharomyces cerevisiae;Selection of axial growth sites in yeast requires Axl2p, a novelplasma membrane glycoprotein;Direct Submission
+JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA
+PUBMED: 7871890;8846915
+SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta
+---
+GENE: AXL2
+FEATURE: gene
+LOCATOR: 687..3158
+LOCUS: SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION: Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p(AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION: U49845
+VERSION: U49845.1 GI:1293613
+KEYWORDS: .
+SOURCE: Saccharomyces cerevisiae (baker's yeast)
+ORGANISM: Saccharomyces cerevisiaeEukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE: 1 (bases 1 to 5028);2 (bases 1 to 5028);3 (bases 1 to 5028)
+AUTHORS: Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.;Roemer,T., Madden,K., Chang,J. and Snyder,M.;Roemer,T.
+TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA damage-induced mutagenesis in Saccharomyces cerevisiae;Selection of axial growth sites in yeast requires Axl2p, a novelplasma membrane glycoprotein;Direct Submission
+JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA
+PUBMED: 7871890;8846915
+SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg
+---
+GENE: AXL2
+NOTE: plasma membrane glycoprotein
+FUNCTION: required for axial budding pattern of S.cerevisiae
+PRODUCT: Axl2p
+PROTEIN_ID: AAA98666.1
+DB_XREF: GI:1293615
+TRANSLATION: MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFTFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQVKDIHGRIPEML
+FEATURE: CDS
+LOCATOR: 687..3158
+LOCUS: SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION: Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p(AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION: U49845
+VERSION: U49845.1 GI:1293613
+KEYWORDS: .
+SOURCE: Saccharomyces cerevisiae (baker's yeast)
+ORGANISM: Saccharomyces cerevisiaeEukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE: 1 (bases 1 to 5028);2 (bases 1 to 5028);3 (bases 1 to 5028)
+AUTHORS: Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.;Roemer,T., Madden,K., Chang,J. and Snyder,M.;Roemer,T.
+TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA damage-induced mutagenesis in Saccharomyces cerevisiae;Selection of axial growth sites in yeast requires Axl2p, a novelplasma membrane glycoprotein;Direct Submission
+JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA
+PUBMED: 7871890;8846915
+SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg
+---
+GENE: REV7
+FEATURE: gene
+LOCATOR: complement(3300..4037)
+LOCUS: SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION: Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p(AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION: U49845
+VERSION: U49845.1 GI:1293613
+KEYWORDS: .
+SOURCE: Saccharomyces cerevisiae (baker's yeast)
+ORGANISM: Saccharomyces cerevisiaeEukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE: 1 (bases 1 to 5028);2 (bases 1 to 5028);3 (bases 1 to 5028)
+AUTHORS: Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.;Roemer,T., Madden,K., Chang,J. and Snyder,M.;Roemer,T.
+TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA damage-induced mutagenesis in Saccharomyces cerevisiae;Selection of axial growth sites in yeast requires Axl2p, a novelplasma membrane glycoprotein;Direct Submission
+JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA
+PUBMED: 7871890;8846915
+SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa
+---
+GENE: REV7
+PRODUCT: Rev7p
+PROTEIN_ID: AAA98667.1
+DB_XREF: GI:1293616
+TRANSLATION: MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQFVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISGDDKILNGVYSQYEEGESIFGSLF
+FEATURE: CDS
+LOCATOR: complement(3300..4037)
+LOCUS: SCU49845 5028 bp DNA PLN 21-JUN-1999
+DEFINITION: Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p(AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION: U49845
+VERSION: U49845.1 GI:1293613
+KEYWORDS: .
+SOURCE: Saccharomyces cerevisiae (baker's yeast)
+ORGANISM: Saccharomyces cerevisiaeEukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE: 1 (bases 1 to 5028);2 (bases 1 to 5028);3 (bases 1 to 5028)
+AUTHORS: Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.;Roemer,T., Madden,K., Chang,J. and Snyder,M.;Roemer,T.
+TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA damage-induced mutagenesis in Saccharomyces cerevisiae;Selection of axial growth sites in yeast requires Axl2p, a novelplasma membrane glycoprotein;Direct Submission
+JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA
+PUBMED: 7871890;8846915
+SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa
+---
--- /dev/null
+ORGANISM: Saccharomyces cerevisiae
+DB_XREF: taxon:4932
+CHROMOSOME: IX
+MAP: 9
+FEATURE: source
+LOCATOR: 1..5028
+ACCESSION: U49845
+SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgat
+---
+PRODUCT: TCP1-beta
+PROTEIN_ID: AAA98665.1
+DB_XREF: GI:1293614
+TRANSLATION: SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM
+FEATURE: CDS
+LOCATOR: <1..206
+ACCESSION: U49845
+SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta
+---
+GENE: AXL2
+FEATURE: gene
+LOCATOR: 687..3158
+ACCESSION: U49845
+SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg
+---
+GENE: AXL2
+NOTE: plasma membrane glycoprotein
+FUNCTION: required for axial budding pattern of S.cerevisiae
+PRODUCT: Axl2p
+PROTEIN_ID: AAA98666.1
+DB_XREF: GI:1293615
+TRANSLATION: MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFTFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQVKDIHGRIPEML
+FEATURE: CDS
+LOCATOR: 687..3158
+ACCESSION: U49845
+SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg
+---
+GENE: REV7
+FEATURE: gene
+LOCATOR: complement(3300..4037)
+ACCESSION: U49845
+SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa
+---
+GENE: REV7
+PRODUCT: Rev7p
+PROTEIN_ID: AAA98667.1
+DB_XREF: GI:1293616
+TRANSLATION: MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQFVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISGDDKILNGVYSQYEEGESIFGSLF
+FEATURE: CDS
+LOCATOR: complement(3300..4037)
+ACCESSION: U49845
+SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa
+---
--- /dev/null
+PRODUCT: TCP1-beta
+PROTEIN_ID: AAA98665.1
+DB_XREF: GI:1293614
+TRANSLATION: SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM
+FEATURE: CDS
+LOCATOR: <1..206
+ACCESSION: U49845
+SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta
+---
+GENE: AXL2
+NOTE: plasma membrane glycoprotein
+FUNCTION: required for axial budding pattern of S.cerevisiae
+PRODUCT: Axl2p
+PROTEIN_ID: AAA98666.1
+DB_XREF: GI:1293615
+TRANSLATION: MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFTFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQVKDIHGRIPEML
+FEATURE: CDS
+LOCATOR: 687..3158
+ACCESSION: U49845
+SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg
+---
+GENE: REV7
+PRODUCT: Rev7p
+PROTEIN_ID: AAA98667.1
+DB_XREF: GI:1293616
+TRANSLATION: MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQFVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISGDDKILNGVYSQYEEGESIFGSLF
+FEATURE: CDS
+LOCATOR: complement(3300..4037)
+ACCESSION: U49845
+SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa
+---
--- /dev/null
+TRANSLATION: SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM
+FEATURE: CDS
+LOCATOR: <1..206
+ACCESSION: U49845
+SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta
+---
+TRANSLATION: MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFTFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQVKDIHGRIPEML
+FEATURE: CDS
+LOCATOR: 687..3158
+ACCESSION: U49845
+SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg
+---
+TRANSLATION: MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQFVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISGDDKILNGVYSQYEEGESIFGSLF
+FEATURE: CDS
+LOCATOR: complement(3300..4037)
+ACCESSION: U49845
+SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa
+---
--- /dev/null
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -i $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -i $in.gz -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -i $in -k AC -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -i $in -k AC -f CDS -O $tmp"
+assert_no_diff $tmp $out.3
+clean
+
+run "$bp -i $in -k AC -f CDS -q translation -O $tmp"
+assert_no_diff $tmp $out.4
+clean
--- /dev/null
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'seq'
+require 'zlib'
+
+# Error class for all exceptions to do with Genbank.
+class GenbankError < StandardError; end
+
+class Genbank
+ include Enumerable
+
+ # Class method allowing open to be used on (zipped) files.
+ # See File.open.
+ def self.open(*args)
+ ios = self.zopen(*args)
+
+ if block_given?
+ begin
+ yield ios
+ ensure
+ ios.close
+ end
+ else
+ return ios
+ end
+ end
+
+ def initialize(io)
+ @io = io
+ @entry = []
+ end
+
+ # Method to close ios.
+ def close
+ @io.close
+ end
+
+ # Iterator method for parsing Genbank entries.
+ def each(hash_keys, hash_feats, hash_quals)
+ while @entry = get_entry do
+ keys = get_keys(hash_keys)
+ seq = get_seq
+
+ features = GenbankFeatures.new(@entry, hash_feats, hash_quals)
+
+ features.each do |record|
+ keys.each_pair { |key,val| record[key] = val }
+ loc = Locator.new(record[:LOCATOR], seq)
+ record[:SEQ] = loc.subseq.seq
+
+ yield record
+ end
+ end
+ end
+
+ private
+
+ # Helper method to return an ios to a file that may be zipped in which case
+ # the ios is unzipped on the fly. See File.open.
+ def self.zopen(*args)
+ ios = File.open(*args)
+
+ begin
+ ios = Zlib::GzipReader.new(ios)
+ rescue
+ ios.rewind
+ end
+
+ self.new(ios)
+ end
+
+ # Method to get the next Genbank entry form an ios and return this.
+ def get_entry
+ block = @io.gets("//" + $/)
+ return nil if block.nil?
+
+ block.chomp!("//" + $/ )
+
+ entry = block.split $/
+
+ return nil if entry.empty?
+
+ entry
+ end
+
+ # Method to get the DNA sequence from a Genbank entry and return
+ # this as a Seq object.
+ def get_seq
+ seq = Seq.new
+ i = @entry.size
+
+ while @entry[i] !~ /^ORIGIN/
+ i -= 1
+ end
+
+ seq.seq = @entry[i + 1 .. @entry.size].join.delete( " 0123456789")
+ seq.type = "dna"
+ seq
+ end
+
+ # Method to get the base keys from Genbank entry and return these
+ # in a hash.
+ def get_keys(hash_keys)
+ keys = {}
+ i = 0
+ j = 0
+
+ while @entry[i] !~ /^FEATURES/
+ if @entry[i] =~ /^\s{0,3}([A-Z]{2})/
+ if want_key?(hash_keys, $1)
+ j = i + 1
+
+ key, val = @entry[i].lstrip.split(/\s+/, 2)
+
+ while @entry[j] !~ /^\s{0,3}[A-Z]/
+ val << @entry[j].lstrip
+ j += 1
+ end
+
+ if keys[key.to_sym]
+ keys[key.to_sym] << ";" + val
+ else
+ keys[key.to_sym] = val
+ end
+ end
+ end
+
+ j > i ? i = j : i += 1
+ end
+
+ keys
+ end
+
+ def want_key?(hash_keys, key)
+ if hash_keys
+ if hash_keys[key.to_sym]
+ return true
+ else
+ return false
+ end
+ else
+ return true
+ end
+ end
+end
+
+class GenbankFeatures
+ @@i = 0
+ @@j = 0
+
+ def initialize(entry, hash_feats, hash_quals)
+ @entry = entry
+ @hash_feats = hash_feats
+ @hash_quals = hash_quals
+ end
+
+ def each
+ while @entry[@@i] and @entry[@@i] !~ /^ORIGIN/
+ if @entry[@@i] =~ /^\s{5}([A-Za-z_-]+)/
+ if want_feat? $1
+ record = {}
+
+ feat, loc = @entry[@@i].lstrip.split(/\s+/, 2)
+
+ @@j = @@i + 1
+
+ while @entry[@@j] and @entry[@@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+ loc << @entry[@@j].lstrip
+ @@j += 1
+ end
+
+ get_quals.each_pair { |k,v|
+ record[k.upcase.to_sym] = v
+ }
+
+ record[:FEATURE] = feat
+ record[:LOCATOR] = loc
+
+ yield record
+ end
+ end
+
+ @@j > @@i ? @@i = @@j : @@i += 1
+ end
+ end
+
+ private
+
+ def get_quals
+ quals = {}
+ k = 0
+
+ while @entry[@@j] and @entry[@@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
+ if @entry[@@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
+ qual = $1
+ val = $2
+
+ if want_qual? qual
+ k = @@j + 1
+
+ while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+ val << @entry[k].lstrip.chomp('"')
+ k += 1
+ end
+
+ if quals[qual]
+ quals[qual] << ";" + val
+ else
+ quals[qual] = val
+ end
+ end
+ end
+
+ k > @@j ? @@j = k : @@j += 1
+ end
+
+ quals
+ end
+
+ def want_feat?(feat)
+ if @hash_feats
+ if @hash_feats[feat.upcase.to_sym]
+ return true
+ else
+ return false
+ end
+ else
+ return true
+ end
+ end
+
+ def want_qual?(qual)
+ if @hash_quals
+ if @hash_quals[qual.upcase.to_sym]
+ return true
+ else
+ return false
+ end
+ else
+ return true
+ end
+ end
+end
+
+
+# Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table locators.
+class LocatorError < StandardError; end
+
+class Locator
+ attr_accessor :locator, :seq, :subseq
+
+ def initialize(locator, seq)
+ @locator = locator
+ @seq = seq
+ @subseq = Seq.new(nil, "", "dna")
+ end
+
+ def subseq
+ parse_locator
+ end
+
+ def to_s
+ @locator
+ end
+
+ private
+
+ # Method that uses recursion to parse a locator string from a feature
+ # table and fetches the appropriate subsequence. the operators
+ # join(), complement(), and order() are handled.
+ # the locator string is broken into a comma separated lists, and
+ # modified if the params donnot balance. otherwise the comma separated
+ # list of ranges are stripped from operators, and the subsequence are
+ # fetched and handled according to the operators.
+ # SNP locators are also dealt with (single positions).
+ def parse_locator(join = nil, comp = nil, order = nil)
+ intervals = @locator.split(",")
+
+ unless balance_params?(intervals.first) # locator includes a join/comp/order of several ranges
+ case @locator
+ when /^join\((.*)\)$/
+ @locator = $1
+ join = true
+ when /^complement\((.*)\)$/
+ @locator = $1
+ comp = true
+ when /^order\((.*)\)$/
+ @locator = $1
+ order = true
+ end
+
+ parse_locator(join, comp, order)
+ else
+ intervals.each do |interval|
+ case interval
+ when /^join\((.*)\)$/
+ @locator = $1
+ join = true
+ parse_locator(join, comp, order)
+ when /^complement\((.*)\)$/
+ @locator = $1
+ comp = true
+ parse_locator(join, comp, order)
+ when /^order\((.*)\)$/
+ @locator = $1
+ order = true
+ parse_locator(join, comp, order)
+ when /^[<>]?(\d+)[^\d]+(\d+)$/
+ int_beg = $1.to_i - 1
+ int_end = $2.to_i - 1
+
+ newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
+ newseq.revcomp if comp
+
+ @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
+ when /^(\d+)$/
+ pos = $1.to_i - 1
+
+ newseq = Seq.new(nil, @seq.seq[pos], "dna")
+ newseq.revcomp if comp
+
+ @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
+ else
+ $stderr.puts "WARNING: Could not match locator -> #{locator}";
+ @subseq.seq << ""
+ end
+ end
+ end
+
+ return @subseq
+ end
+
+ def balance_params?(locator)
+ parens = 0
+
+ locator.each_char do |char|
+ case char
+ when '(' then parens += 1
+ when ')' then parens -= 1
+ end
+ end
+
+ if parens == 0
+ return true
+ else
+ return false
+ end
+ end
+end
+
+
+__END__
--- /dev/null
+#!/usr/bin/env ruby
+
+require 'genbank'
+require 'seq'
+require 'test/unit'
+require 'pp'
+
+class TestGenbank < Test::Unit::TestCase
+ def setup
+ seq = Seq.new(nil, "tcatgatcaagatctaacagcagaagtacacttctattta", "dna")
+ @loc = Locator.new("", seq)
+ end
+
+ def test_Locator_with_single_position_returns_correctly
+ @loc.locator = "10"
+ assert_equal("a", @loc.subseq.seq)
+ end
+
+ def test_Locator_with_single_interval_returns_correctly
+ @loc.locator = "5..10"
+ assert_equal("gatca", @loc.subseq.seq)
+ end
+
+ def test_Locator_with_multiple_intervals_return_correctly
+ @loc.locator = "5..10,15..20"
+ assert_equal("gatcataaca", @loc.subseq.seq)
+ end
+
+ def test_Locator_with_join_multiple_intervals_return_correctly
+ @loc.locator = "join(5..10,15..20)"
+ assert_equal("gatcataaca", @loc.subseq.seq)
+ end
+
+ def test_Locator_with_complement_and_single_interval_return_correctly
+ @loc.locator = "complement(5..10)"
+ assert_equal("tgatc", @loc.subseq.seq)
+ end
+end
+
+
+__END__
projects / biopieces.git / commitdiff