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Article #2414Problem with -l option in blast
From: Bansal Parit
Date: Thu, 25 Feb 2010 17:17
Date: Thu, 25 Feb 2010 17:17
28 lines
3703 bytes
3703 bytes
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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