[BiO BB] questions on blast

[Huang Tao]

Apparently, I make a mistake:)
So, please omit it.

2008/5/29 Huang Tao <silkhuang at gmail.com>:

> 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




-- 
黄韬， Tao Huang