[BiO BB] questions on blast

[Xiaowei Jiang]

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: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org]
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

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