Apparently, I make a mistake:) So, please omit it. 2008/5/29 Huang Tao <[EMAIL PROTECTED]>:
> 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 <[EMAIL PROTECTED]>: > > 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 >> >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > 黄韬， Tao Huang -- 黄韬， Tao Huang _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
