[BiO BB] questions on blast
silkhuang at gmail.com
Thu May 29 19:18:00 EDT 2008
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 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
> BBB mailing list
> BBB at bioinformatics.org
黄韬， Tao Huang
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