[Bio-software] Problem with -l option in blast

Bansal Parit via bio-soft%40net.bio.net (by bansalp from student.ethz.ch)
Thu Feb 25 12:17:48 EST 2010


Hi,

I am trying to use -l option to restrict the blast search to a list of GI's. For doing this I downloaded the swissprot database (FASTA file) from the BLAST FTP site and ran formatdb on it with -p T -o T options. Then I took the sequence mentioned below and did a blastall -p blastp without the -l option. This gave me a result file with a number of hits. From these hits I picked one and went back to the FASTA file and retrived the GI corresponding to it. Then I wrote this GI in a .gi file and again ran blastall with -l option. Now it should only restrict the search to this particular GI but instead I get the following error:

[blastall] ERROR: gi|2507261|sp|P00496|PUR1_ECOLI: Unable to open file seqlist2.gi
[blastall] WARNING: gi|2507261|sp|P00496|PUR1_ECOLI: Intersection of gilist and BLAST database ID's empty

Where seqlist2.gi contains the GI 84029594.

FASTA query was : 

>gi|2507261|sp|P00496|PUR1_ECOLI Amidophosphoribosyltransferase (Glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (GPATASE)
MCGIVGIAGVMPVNQSIYDALTVLQHRGQDAAGIITIDANNCFRLRKANGLVSDVFEARHMQRLQGNMGI
GHVRYPTAGSSSASEAQPFYVNSPYGITLAHNGNLTNAHELRKKLFEEKRRHINTTSDSEILLNIFASEL
DNFRHYPLEADNIFAAIAATNRLIRGAYACVAMIIGHGMVAFRDPNGIRPLVLGKRDIDENRTEYMVASE
SVALDTLGFDFLRDVAPGEAIYITEEGQLFTRQCADNPVSNPCLFEYVYFARPDSFIDKISVYSARVNMG
TKLGEKIAREWEDLDIDVVIPIPETSCDIALEIARILGKPYRQGFVKNRYVGRTFIMPGQQLRRKSVRRK
LNANRAEFRDKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLASAAPEIRFPNVYGIDMPSATELIAHG
REVDEIRQIIGADGLIFQDLNDLIDAVRAENPDIQQFECSVFNGVYVTKDVDQGYLDFLDTLRNDDAKAV
QRQNEVENLEMHNEG


I could not comprehend the reason for this behaviour here and any help would be appreciated.

Thankx

Regards,
Parit Bansal



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