Open source All vs All Blast script?

Question

[lufiealf]

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

Thank you

[DG]

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

[lufiealf]

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

Answer 1

[Asaf]

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.

[DG]

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

Answer 2

[Pierre Lindenbaum]

LAST is able to compare two vertebrate genomes

[lufiealf]

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

[DG]

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