[BiO BB] questions on blast

[Martin Gollery]

Hi
The X's are an indication that the sequence has been filtered for low
complexity data by the filtering program SEG.

Best regards,
Marty


On Thu, May 29, 2008 at 9:06 AM, Xue Li <me.lixue at gmail.com> 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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> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
TimeLogic- a Division of Active Motif
775-833-9113
880 Northwood Blvd. Suite 7
Incline Village, NV 89451