[BiO BB] questions on blast
idh at poulet.org
Fri May 30 07:40:18 EDT 2008
the Xs are probably sequence that was filtered out... it could
example be a "low complexity" repeat.
Databases are constantly being updated... and sometimes there are
several versions (with more or less redundancy).
yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
On May 29, 2008, at 18:06 , Xue Li wrote:
> 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
> Sbjct: 1
> SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60
> Would someone please tell me what do the Xs mean in the query
> 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
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> BBB at bioinformatics.org
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