8 I would like to encorporate some domain-specific compression algorithm. Options
10 * G-SQZ (http://www.tgen.org/research/gsqueez.cfm) : not open source (i.e. not an option)
11 * fqzcomp (http://seqanswers.com/forums/archive/index.php/t-6349.html)
12 * DSRC (http://bioinformatics.oxfordjournals.org/cgi/content/short/27/6/860?rss=1) :
38 Specifying the score matrix, rather than using a hardcoded.
40 The implementation of the Smith-Waterman algorithm could be more efficient. We
41 might look to Phil Green's cross_match implementation for ideas.
43 An option to return the sequences that match past a certain threshold would be