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SOP031: Finding a Degenerate Peptide Motif in Selected Organisms

This procedure explains how to use the NMPDR ToolSearch (BLAST or Scan in the NmpdrBanner) to find a particular type of DNA sequence in one or more of our genomes.

First, select the BLAST or Scan search option. This is the search page for locating sequence data.

We're searching for a protein pattern, so you want to select the protScan tool from the dropdown list.

Type the motif of interest in the sequence box.

  • For example, use a collagen-binding motif implicated in acute rheumatic fever (ARF) following streptococcal infection, AXYLXXN (icon J Biol Chem 282:18686). The X characters will match any amino acid.

Select the genomes to search in the genome list.

  • For example, select all strains of Streptococcus pyogenes from the genomes list quickly by typing pyogenes in the text box and clicking Select genomes containing.

Now click the SCAN button.

Features with matching sequences are presented in a table with links to respective FIG.GenomeViewer? pages.

Search results from the protein pattern scan
In the three results above, one shows a matching AEYLKGLN sequence and the other two match with AAYLDDLN.

Use the form below to try the example, or to attempt your own search. The results will open in a new tab or window.

Protein Search Pattern
Select one or more genomes
  
SopForm
Number 031
Audience UserGroup
Title Finding a Degenerate Peptide Motif in Selected Organisms
Style active
Topic revision: r5 - 18 Aug 2008 - 15:31:24 - BruceParrello
 
NMPDR is a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.