[BiO BB] questions on blast
silkhuang at gmail.com
Fri May 30 20:25:41 EDT 2008
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
> Btw, you may try BLAST service in RCSB PDB, you will find more hits.
> 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
>> Identities = 596/637 (93%), Positives = 596/637 (93%)
>> Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60
>> SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR
>> Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR
>> 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
>> BBB mailing list
>> BBB at bioinformatics.org
> 黄韬， Tao Huang
黄韬， Tao Huang
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