Re: blastall problem

hi Torsten,  

blastall -p blastp -i result/fasta.faa -d /export/home/database/nr works

perfectly fine on the command line, and the 'fasta.faa' is in fasta format:

gi|18676474|dbj|BAB84889.1| FLJ00134 protein [Homo sapiens]

HLSAQKASVGPESVSGLGTRTWPRVSCEVTVQCWPGCHLKVGGFKMAPWQGVGRRPWFLTWGPLCGAASVSPSMTVASSQ

QGWDCTAGRRWLGEGEIEALAQVSEFKTVLSFQGPAASPDGSSATRVPQDVTQGPGATGGKEDSGMIPLAGTAPGAEGPA

PGDSQAVRPYKQEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHLLRHRQSHSGEKPHACPECGKAFRRKEHLRRHR

DTHPGSPGSPGPALRPLPAREKPHACCECGKTFYWREHLVRHRKTHSGARPFACWECGKGFGRREHVLRHQRIHGRAAAS

AQGAVAPGPDGGGPFPPWPLG

it seems like i'm just one bloody step away from success. ^ ^* can't figure

out the prob. 

thanks for your help.

Torsten Seemann wrote:

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

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