Blastall help !!!

[empyrean]

Hello All,

I need some help in optimizing my blastall query. I have a file of 10000 genes, and i wanted to blast them against themselves. So, i created blast db to perform blastall. But i dont want the genes that map to themselves. I would like to get second best hit from the results. Can i do this in blastall using some parameters or do i need to write a perl script for this?

blastall -p blastn -m 9 -d testgenesdb -i test.fasta -o outputtest.QUERY

That is the query i uses and it brings out blast results in tabular format..
please help me if u know optimizing blast queries.

Thank you all

[klaas.vandepoele]

example

code exclude_self.pl

while (<STDIN>)
{
my @l= split(/\t/,$_);
if ($l[0] ne $l[1])
{
print join("\t",@l)."\n";
}
}


--

perl exclude_self.pl < outputtest.QUERY > outputtest.QUERY.noself

Something like this should work.

best,
Klaas

[empyrean]

Thank you for the code.. this is what i wanted but i need only second best hit.. i dont want all the results...how can i achieve it?

[empyrean]

How to get the second best hit or after running above code, i need the first row with best evalue for all the combinations..