Question: Blasting against multiple fasta file
0
gravatar for srogers
3.2 years ago by
srogers0
srogers0 wrote:

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

genome • 1.3k views
ADD COMMENTlink modified 3.2 years ago by genomax65k • written 3.2 years ago by srogers0
1

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 3.2 years ago • written 3.2 years ago by genomax65k
5
gravatar for Benn
3.2 years ago by
Benn6.6k
Netherlands
Benn6.6k wrote:

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.

ADD COMMENTlink written 3.2 years ago by Benn6.6k
0
gravatar for genomax
3.2 years ago by
genomax65k
United States
genomax65k wrote:

I would also include "blat": https://genome.ucsc.edu/FAQ/FAQblat.html#blat3

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 3.2 years ago • written 3.2 years ago by genomax65k
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