Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Reformatting BLAST+ pairwise alignment? Genomics101 Bioinformatics 2 12-05-2013 02:53 AM
FDR in RNA-Seq with Multiple Pairwise Tests NateP Bioinformatics 1 10-22-2012 08:10 AM
fastest pairwise alignment method Trilliput Bioinformatics 0 10-19-2012 11:59 AM
multiple pairwise comparisons in DESeq and/or edgeR sjm RNA Sequencing 0 03-31-2012 08:12 AM
Multiple Alignment software for huge amount of peptide sequences/cysteine framework LucasVS Bioinformatics 3 03-28-2012 07:15 PM

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

Join Date: Oct 2012
Posts: 10
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?

rdoan is offline   Reply With Quote
Old 12-25-2013, 03:22 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

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.
maubp is offline   Reply With Quote

alignment, bioinformatics, conservation, evolutionary biology, pairwise

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:43 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO