BSSB contains three derived databases for all PDB sequences and 25% & 90% non-redundant protein sequences. Choose a database and paste the query sequence to blast it or click 'browse' to upload a query sequence from the system. Give a set of subsequences if you do not want to blast the entire query sequence.
Database : PDB (All structures) PDB (Non-homologous 25%) PDB (Non-homologous 90%) Program : blastp
Enter a protein sequence below (Example) Or load it from disk
Set subsequence: From To
ALGORITHM PARAMETERS (optional)
No.of sequence to be displayed: 10 20 50 100 500 1000 2000 No.of Alignments to be displayed: 10 20 50 100 500 1000 2000 Expect threshold: Choose Matrix: PAM30 PAM70 BLOSUM80 BLOSUM62 BLOSUM45 Gap costs: Existense:11,Extension:1 Existense:11,Extension:2 Existense:10,Extension:2 Existense:12,Extension:1 Existense:9,Extension:2 Existense:8,Extension:2 Existense:10,Extension:1 Existense:7,Extension:2 Existense:6,Extension:2 Existense:9,Extension:2 ungapped alignment Existense:11,Extension:2 Existense:10,Extension:2 Existense:12,Extension:2 Existense:9,Extension:1 Existense:8,Extension:2 Existense:11,Extension:1 Existense:10,Extension:2 Existense:7,Extension:1 Existense:6,Extension:2 ungapped alignment Existense:13,Extension:2 Existense:16,Extension:2 Existense:15,Extension:1 Existense:19,Extension:2 Existense:12,Extension:2 Existense:18,Extension:1 Existense:14,Extension:1 Existense:11,Extension:2 Existense:13,Extension:2 Existense:17,Extension:1 Existense:10,Extension:3 Existense:16,Extension:1 Existense:12,Extension:2 ungapped alignment Existense:10,Extension:1 Existense:7,Extension:2 Existense:6,Extension:2 Existense:9,Extension:1 Existense:5,Extension:2 Existense:8,Extension:1 ungapped alignment Existense:8,Extension:2 Existense:11,Extension:1 Existense:7,Extension:2 Existense:10,Extension:1 Existense:6,Extension:2 Existense:9,Extension:1 Wordsize: 3 2 Filter: Low complexity regions Mask: Mask lower case letters