Blast Protein Blast Protein icon

Blast Protein performs protein sequence searches using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). Corresponding structures can be retrieved and automatically superimposed, and the pseudo-multiple alignment from BLAST can be shown in Multalign Viewer. The search results are included in saved sessions. See also: mda

There are several ways to start Blast Protein, a tool in the Sequence category. When it is started from the Info menu in Multalign Viewer, any of the sequences in the alignment can be specified as the query. Otherwise, the query sequence can be:

Search parameters: Clicking OK launches the search and dismisses the dialog. Apply launches the search without dismissing the dialog, Cancel simply dismisses the dialog, and Help opens this manual page in a browser window.

The search is a background task. Clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired.

Blast Results

Results are returned as a table of sequences with several columns of information. Which columns are displayed can be set in the Column configuration panel.

Some columns of information are available for nr sequences regardless of whether they are in the pdb subset:

Additional columns are available for pdb sequences:

Other than PDB identifier, the information in these columns is retrieved using a web service provided by the RCSB PDB.

One or more of the hits (lines in the table) can be chosen with the left mouse button. A block of lines can be chosen by dragging, or by clicking on the first (or last) line in the desired block and then Shift-clicking on its last (or first) line. Ctrl-click toggles the state (chosen or not) of single line.

Buttons at the bottom of the results dialog:


Basic Local Alignment Search Tool (BLAST). The BLAST software is provided by the NCBI and described in the following:

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.

Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. J Mol Biol. 1990 Oct 5;215(3):403-10.

Pseudo-multiple alignment. The pseudo-multiple alignment from BLAST is not a true multiple alignment, but a consolidation of the pairwise alignments of individual hits to the query. This output corresponds to the BLAST formatting option (alignment view) "flat query-anchored without identities," in which identities and conservative changes relative to the query are shown in upper case, nonconservative changes in lower case.

UCSF Computer Graphics Laboratory / May 2012