Question: Blasting against multiple fasta file
gravatar for srogers
4.1 years ago by
srogers0 wrote:


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!


genome • 1.6k views
ADD COMMENTlink modified 4.1 years ago by genomax80k • written 4.1 years ago by srogers0

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?

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by genomax80k
gravatar for Benn
4.1 years ago by
Benn7.9k wrote:

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

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

ADD COMMENTlink written 4.1 years ago by Benn7.9k
gravatar for genomax
4.1 years ago by
United States
genomax80k wrote:

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.

ADD COMMENTlink modified 11 weeks ago by RamRS26k • written 4.1 years ago by genomax80k
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