Blast Protein

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:

• From Structure - a protein chain from a structure open in Chimera
• Plain Text - a protein sequence entered or pasted in the Sequence field as plain text

• Program
  • blast (default) - protein-protein search
  • psiblast - iterated protein-protein search, where each pass after the first uses a PSSM (position-specific scoring matrix) based on the results of the previous pass
• Database
  • pdb (default) - sequences of structures in the Protein Data Bank (PDB). Whereas completely identical sequences are collapsed to a single entry in the pdb sequence database from NCBI, the RBVI Web service uses a customized version of this database in which the identical sequences are separate entries. The List only... option controls whether multiple hits with the same PDB identifier or only the best-matching one should be included in the results.
  • nr - all non-redundant GenBank CDS translations + RefSeq Proteins + PDB + SwissProt + PIR + PRF. This database is much larger than pdb and will take longer to search.
• E-value (1e-X) - significance cutoff; only matches with E-values ≤ 10^-X will be returned (X=3 by default)
• Matrix (BLOSUM45/BLOSUM62/BLOSUM80/PAM30/PAM70) - amino acid substitution matrix to use for alignment scoring
• Passes (default 1) - number of psiblast iterations; 1 pass is equivalent to blast, whereas multiple passes will find more distantly related sequences
• List only best-matching chain per PDB entry (default) - whether multiple hits with the same PDB identifier (matches to different chains in that PDB entry) or only the best-matching one should be included in the results

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:

• GI - sequence GI number (for the query, model name is shown instead)
• PDB - corresponding PDB identifier, if any
• Evalue - significance value
• Score - alignment score
• Description - text description

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.

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."