[Bioperl-l] blastall problem

[Torsten Seemann]

Dorjee,

> thanks alot for your reply again. as per your suggestion (using 'die "could
> not get seq" if not defined $queryin;'), i now get the following error
> message:
> Software error:
> could not get seq at /usr/local/apache2/htdocs/remote_ncbi.pl line 50.
> i've attached the script. could you plz have a look at it and see where am i
> going wrong.
> cheers mate!

This strongly suggests that your FASTA file is not actually in FASTA format.
http://en.wikipedia.org/wiki/Fasta_format

Does it work if you pass it to blastall on the command line?
eg. blastall -p blastp -i result/fasta.faa -d /export/home/database/nr

> Saier Lab.
> 858-534-2457

Are you working at UCSD?

--Torsten