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FASTA TEST DATA FILES ===================== This directory contains various data files for testing the Fasta-related code in Biopython. The following are the common sequence file format, originally introduced as the input file format for Bill Pearson's FASTA tools. These are for tested in Bio.SeqIO and Bio.AlignIO (where the format is called "fasta") as well as other older parts of Biopython such as the Bio.Fasta module. ID Description f001 1 protein sequence f002 3 DNA sequences f003 2 proteins, with comments fa01 fasta alignment The following are example "machine readable" pairwise alignment output files from the FASTA tools when using the -m 10 command line option. These are for testing the Bio.AlignIO and Bio.SearchIO code where the format is called "fasta-m10". output001.m10 - fasta35 protein-protein, 3 query sequences, no histogram, with expectation threshold output002.m10 - fasta34 protein-protein, 3 query sequences, with offsets and word size, max 2 hits per query output003.m10 - fasta34 protein-protein, 5 query sequences, very strict threshold so not all have hits. output004.m10 - fasta35 nucleotide-nucleotide, 3 queries where only the middle one has a single hit. output005.m10 - ssearch35 protein-protein, 3 queries where only the middle one has a single hit. output006.m10 - fasta35 nucleotide-nucleotide, 1 query, in the alignment the query has been reversed. output007.m10 - recreation of output001.m10 using fasta-36.3.4 (note that histogram is now off by default, -H now turns it on, and the -Q quiet flag no longer exists). Get more hits due to revised e-value calculations, also ">>><<<" marks end of a query, not just end of the file! output008.m10 - tfastx36 protein-nucleotide, 4 queries, some with no hits, some matches with multiple HSPs (new feature in FASTA v36) output009.m10 - fasta36, multiple dna queries output010.m10 - fasta36, single dna query, no hit output011.m10 - fasta36, single dna query, each hit contains a single hsp output012.m10 - fasta36, single dna query, some hits contain multiple hsps output013.m10 - fasta36, multiple protein queries output014.m10 - fasta36, single protein query, no hit output015.m10 - fasta36, single protein query, each hit contains a single hsp output016.m10 - fasta36, single protein query, some hits contain multiple hsps