[BiO BB] questions on blast

Yannick Wurm idh at poulet.org
Fri May 30 07:40:18 EDT 2008


Hi Xue,

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).

good luck,

yannick
-------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html
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
>                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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