[BiO BB] questions on blast

Huang Tao silkhuang at gmail.com
Thu May 29 19:18:00 EDT 2008


Xs mean gaps, which can be considered as 'insertion' or 'deletion' in
biology.

Btw, you may try BLAST service in RCSB PDB, you will find more hits.
http://www.rcsb.org/pdb/search/searchSequence.do


2008/5/29 Xue Li <me.lixue at gmail.com>:

> 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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> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
黄韬, Tao Huang


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