Align two fasta files against each other

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4.7 years ago

Palgrave ▴ 110

I have two files File1.fa and File2.fa that I would like to align against each other. I would like to print only the alignment result for File1 and leave a gap (-) where File1 does not align to File2.

Which tools and parameters would you choose?

alignment • 5.3k views

ADD COMMENT • link 4.7 years ago by Palgrave ▴ 110

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What have you tried already?

You need to be a bit more specific: - Are you interested in local or global alignments? - Do you want all-vs-all alignment? - What are you defining as 'not aligning'?

ADD REPLY • link 4.7 years ago by Joe 21k

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Go to BLAST align 2 sequences, paste your sequences, adjust program selection, and you will get an alignment in couple of seconds. Gaps can be adjusted manually afterwards.

ADD REPLY • link 4.7 years ago by Mensur Dlakic ★ 27k

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I have two large files containing about 10000 fasta sequences. I would like to output one alignment for each sequence in File1. I guess command line blast is better? What parameters should I use?

ADD REPLY • link 4.7 years ago by Palgrave ▴ 110

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Try needle or water, for global or local alignment respectively, from the EMBOSS command line package.

ADD REPLY • link 4.7 years ago by Benn 8.3k

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