compare two fasta files

Question

[samuel]

I have two large files with fasta sequences (~3000 each). I can't quite get things to work by blasting two sequences : https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

I was wondering if anyone else had solved a similar problem. I'm very new to BI and have very limited programming skills so any advice would be awesome.

Thanks.

[samuel]

BTW I want to compare the two files and find any sequences that match

Answer 1

[Petr Ponomarenko]

Install blastn https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Run one file against the other (help is here https://www.ncbi.nlm.nih.gov/books/NBK279675/ or use blastn --help)

blast -query file1.fasta -subject file2.fasta -outfmt 6 -out results.txt

outfit 6 is for tabular output that most of us begin with as it easy to load to other software.

Change your alignment and filtration parameters according to your task

Have not tested on 3k reads against 3k reads. If it does not work out, make a database out of one of the files and run with -db parameter instead of -subjects parameter

[samuel]

Thanks for your help Petr!