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.

** In the Mac Aqua version of the Chimera 1.4 release, it is necessary to wait until the Blast search is done before resuming work with Chimera. ** Trying to access the menus while a background job (the Blast search) is running causes the program to freeze. A 1.4.1 release that fixes this problem is planned. In the meanwhile, the psiblast and database nr options are disabled in the Mac Aqua version only.

There are several ways to start Blast Protein, a tool in the Sequence category. 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.

Results are returned as a table of sequences with the following columns:

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. Show in MAV displays the pseudo-multiple alignment of the chosen sequences in Multalign Viewer, and Load Structure retrieves and opens the PDB structures corresponding to the chosen sequences (as described for Fetch by ID) and automatically superimposes them according to the pseudo-multiple alignment. Entire PDB entries are retrieved, not just the matching chains.

Quit removes the table of results, whereas Hide undisplays it without removing the data. The hidden table can be shown again using the Raise option of its instance in the Tools menu. This is also useful when the table has become obscured by other windows.

Notes

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 with letters for identities."


UCSF Computer Graphics Laboratory / November 2009