Hi XUE, You can simply turn the filter option off.
By default, you have the following parameters set, when you use NCBI BLAST stand alone program. ------------------------------------------ blastall -p blastp -d nr -i stdin -e 10 -m 0 -o stdout -F T -G 11 -E 2 -X 15 -v 500 -b 250 -f 11 -g T -a 1 -M BLOSUM62 -W 3 -z 0 -K 0 -Y 0 -T F -U F -y 0.0 -Z 0 -A 40 ------------------------------------------- The option "-F" which filters the query sequence for low-complexity subsequences. You can simply turn this option off by using <-F "">. Please check NCBI BLAST documentation for detail! Regards, Xiaowei -------------------- Smurfit Institute of Genetics University of Dublin, Trinity College, Ireland -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Xue Li Sent: 29 May 2008 17:07 To: General Forum at Bioinformatics.Org Subject: [BiO BB] questions on blast Hello all, I installed blast-2.2.18 on my Ubuntu, and did blastp on 1RREQ_B.fasta.txt on pdb database. I got the following results: Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based stats. Identities = 596/637 (93%), Positives = 596/637 (93%) Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 Would someone please tell me what do the Xs mean in the query sequence? Also, the results is different from the NCBI blast result. I downloaded pdb database today. Local Blast results show that there are 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in pdb database. Even I installed blast-2.2.18, local Blast results show that I am using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. Did I do something wrong? -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
