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-Introduction
-
-The Smith-Waterman [1] algorithm is one of the most sensitive sequencing
-algorithms in use today. It is also the slowest due to the number of
-calculations needed to perform the search. To speed up the algorithm, it
-has been adapted to use Single Instruction Multiple Data, SIMD, instructions
-found on many common microprocessors today. SIMD instructions are able to
-perform the same operation on multiple pieces of data parallel.
-
-The program swsse2 introduces a new SIMD implementation of the Smith-Waterman
-algorithm for the X86 processor. The weights are precomputed parallel to the
-query sequence, like the Rognes [2] implementation, but are accessed in the
-striped pattern. The new implementation reached speeds six times faster than
-other SIMD implementations.
-
-Below is a graph comparing the total search times of 11 queries, 3806 residues,
-against the Swiss-Prot 49.1 database, 75,841,138 residues. The tests were run
-on a PC with a 2.00GHz Intel Xeon Core 2 Duo processor with 2 GB RAM. The
-program is singlely threaded, so the number of cores has no affect on the run
-times. The Wozniak, Rognes and striped implementations were run with the
-scoring matrices BLOSUM50 and BLOSUM62 and four different gap penalties, 10-k,
-10-2k, 14-2k and 40-2k. Since the Wozniak's runtime does not change depending
-on the scoring matrix, one line is used for both scoring matrices.
-
-Build Instructions
-
- * Download the zip file with the swsse2 sources.
- * Unzip the sources.
- * Load the swsse2.vcproj file into Microsoft Visual C++ 2005.
- * Build the project (F7). For optimized code, be sure to change the
- configuration to a Release build.
- * The swsse2.exe file is in the Release directory ready to be run.
-
-Running
-
-To run swsse2 three files must be provided, the scoring matrix, query sequence
-and the database sequence. Four scoring matrices are provided with the
-release, BLOSUM45, BLOSUM50, BLOSUM62 and BLOSUM80. The query sequence and
-database sequence must be in the FASTA format. For example, to run with the
-default gap penalties 10-2k, the scoring matrix BLOSUM50, the query sequence
-ptest1.fasta and the sequence database db.fasta use:
-
- c:\swsse2>.\Release\swsse2.exe blosum50.mat ptest1.fasta db.fasta
- ptest1.fasta vs db.fasta
- Matrix: blosum50.mat, Init: -10, Ext: -2
-
- Score Description
- 53 108_LYCES Protein 108 precursor.
- 53 10KD_VIGUN 10 kDa protein precursor (Clone PSAS10).
- 32 1431_ECHGR 14-3-3 protein homolog 1.
- 32 1431_ECHMU 14-3-3 protein homolog 1 (Emma14-3-3.1).
- 27 110K_PLAKN 110 kDa antigen (PK110) (Fragment).
- 26 1432_ECHGR 14-3-3 protein homolog 2.
- 25 13S1_FAGES 13S globulin seed storage protein 1
- 25 13S3_FAGES 13S globulin seed storage protein 3
- 25 13S2_FAGES 13S globulin seed storage protein 2
- 23 12S1_ARATH 12S seed storage protein CRA1
- 22 13SB_FAGES 13S globulin basic chain.
- 21 12AH_CLOS4 12-alpha-hydroxysteroid dehydrogenase
- 21 140U_DROME RPII140-upstream protein.
- 21 12S2_ARATH 12S seed storage protein CRB
- 21 1431_LYCES 14-3-3 protein 1.
- 20 1431_ARATH 14-3-3-like protein GF14
-
- 21 residues in query string
- 2014 residues in 25 library sequences
- Scan time: 0.000 (Striped implementation)
-
-Options
-
- Usage: swsse2 [-h] [-(n|w|r|s)] [-i num] [-e num] [-t num] [-c num]
- matrix query db
-
- -h : this help message
- -n : run a non-vectorized Smith-Waterman search
- -w : run a vectorized Wozniak search
- -r : run a vectorized Rognes search (NOT SUPPORTED)
- -s : run a vectorized striped search (default)
- -i num : gap init penalty (default -10)
- -e num : gap extension penalty (default -2)
- -t num : minimum score threshold (default 20)
- -c num : number of scores to be displayed (default 250)
- matrix : scoring matrix file
- query : query sequence file (fasta format)
- db : sequence database file (fasta format)
-
-Note
-
-The Rognes implementation is not released as part of the swsse2 package due to
-patent concerns.
-
-References
-
-[1] Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
-[2] Rognes, T. and Seeberg, E. (2000) Six-fold speed-up of the Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics, 16, 699-706.
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projects / fastq-tools.git / blobdiff