Blasting against multiple fasta file

Question

[srogers]

Hi

I have a single fasta file that contains just over 70,000 individual sequences from a non-model organism (no genome available). I would like to Blast four different known gene sequences against this file/these sequences. I'm not in a bioinformatics lab so any approach has to use free software please (I have Sequencher).

This is probably a really basic question for this forum but help appreciated!

Thanks

[GenoMax]

What kind of hardware do you have access to (unix preferable/may be the only thing practical in terms of free options with this size data set)? Do you have any experience with command line? What is the size of the 70K dataset file?

Answer 1

[Benn]

You'll have to download the stand alone blast tool from NCBI.

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

You can make a DB from the 70k fasta file, and then you can blast your four genes to this DB.

Answer 2

[GenoMax]

I would also include blat

There would be no need to make indexes beforehand unless 70k data is very large. It is possible to get output in "blast" format if you prefer that.

I should add that blat would work as long as the sequences being compared are evolutionarily close (highish % identity) otherwise blast is the better option.