[BiO BB] questions on blast
me.lixue at gmail.com
Thu May 29 12:06:41 EDT 2008
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
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
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?
Bioinformatics and Computational Biology program @ ISU
Ames, IA 50010
More information about the BBB