[BiO BB] questions on blast

Xue Li me.lixue at gmail.com
Thu May 29 12:06:41 EDT 2008


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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