VistaPDB Manual -> Alignments -> BLAST

BLAST Alignments

VistaPDB can align primary 'query' sequences to primary sequences in PDB files.

1) To BLAST align a primary sequence against the NCBI PDB structure file database, go to Tools -> Blast Sequence against PDB Database.

2) Enter a sequence into the text box provided. Blast parameters can be altered by clicking the arrow next to preferences.

3) Blast results will appear as both a list of PDB file hits and the alignments created by NCBI.

4) To download a PDB file, select a file in the list for download.

5) Upon download, a new viewer will open with the recently downloaded file, together with the primary sequences aligned. Red indicates mismatches, blue incicates changes to similar resides based upon the BLOSUM62 matrix, and black indicates identical residues.