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Old 12-24-2013, 11:37 AM   #1
rdoan
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Location: USA

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Default Pairwise alignment of multiple sequences

Hello, I would like to perform a pairwise alignment between 100 samples that each contain about 2,000 sequences from different genomic regions. What I would like is the percent identity (ID) at each of the 2,000 sequences between the 100 samples and a reference set of 2,000 sequences (total of 200,000 % ID values). Are there any recommended programs to perform this large batch of alignments while extracting the % ID or number of similar/different bases?

Thanks,
Ryan
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Old 12-25-2013, 03:22 AM   #2
maubp
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BLAST+ can do pairwise searching (FASTA file versus FASTA file), which might be what you want.

Also EMBOSS has various pairwise alignment tools, e.g.
http://emboss.sourceforge.net/apps/r...needleall.html
http://emboss.sourceforge.net/apps/r...ps/needle.html
http://emboss.sourceforge.net/apps/r...pps/water.html
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alignment, bioinformatics, conservation, evolutionary biology, pairwise

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