Question: Open source All vs All Blast script?
0
gravatar for lufiealf
3.3 years ago by
lufiealf0
United States
lufiealf0 wrote:

I am looking to an all vs all blast between two genomes, does anyone know of a script that does this?

Thank you

 

blast genome • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Asaf5.5k • written 3.3 years ago by lufiealf0

Are you looking to do just the single-way comparison or reciprocal BLAST? 

ADD REPLYlink written 3.3 years ago by Dan Gaston7.1k
1
gravatar for Pierre Lindenbaum
3.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

LAST http://last.cbrc.jp/ is able to compare two vertebrate genomes

 

 

ADD COMMENTlink written 3.3 years ago by Pierre Lindenbaum119k

Do you know of anything to All v All compare invertebrate genomes?

ADD REPLYlink written 3.3 years ago by lufiealf0

It should work for invertebrates as well. It isn't restricted to vertebrate genomes. The only limiting factor is really the size of the genomes you are comparing to each other

ADD REPLYlink written 3.3 years ago by Dan Gaston7.1k
1
gravatar for Asaf
3.3 years ago by
Asaf5.5k
Israel
Asaf5.5k wrote:

You just have to have two fasta files of e.g. proteins of the two genomes, you run formatdb on one of them and then run blastall with one fasta as input file (-i) and the other as database (-d). Use -m8 to get the output in tabular format and you'll get a tab-delimited file with all against all proteins.

ADD COMMENTlink written 3.3 years ago by Asaf5.5k

Although if you want reciprocal best hits, which you often do, you have to do the other comparison and then compare the two results. 

ADD REPLYlink written 3.3 years ago by Dan Gaston7.1k
0
gravatar for lufiealf
3.3 years ago by
lufiealf0
United States
lufiealf0 wrote:

Do you know of anything to All v All compare invertebrate genomes?

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by lufiealf0
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