CompariMotif is a piece of software with a single objective: to take two lists of protein motifs and compare them to each other, identifying which motifs have some degree of overlap, and identifying the relationships between those motifs. It can be used to compare a list of motifs with themselves, their reversed selves, or a list of previously published motifs, for example (e.g. ELM (http://elm.eu.org/)). CompariMotif outputs a table of all pairs of matching motifs, along with their degree of similarity (information content) and their relationship to each other.
The best match is used to define the relationship between the two motifs. These relationships are comprised of the following keywords:
Match type keywords identify the type of relationship seen:
Exact = all the matches in the two motifs are precise Variant = focal motif contains only exact matches and subvariants of degenerate positions in the other motif Degenerate = the focal motif contains only exact matches and degenerate versions of positions in the other motif Complex = some positions in the focal motif are degenerate versions of positions in the compared motif, while others are subvariants of degenerate positions. Match length keywords identify the length relationships of the two motifs:
Match = both motifs are the same length and match across their entire length Parent = the focal motif is longer and entirely contains the compared motif Subsequence = the focal motif is shorter and entirely contained within the compared motif Overlap = neither motif is entirely contained within the other This gives sixteen possible classifications for each motif's relationship to the compared motif.
Availability & Contact
COMPARIMOTIF can be run, with some limitations, from the Webserver.
COMPARIMOTIF is freely available for local installation under a GNU General Public License as a standalone download and part of the PEAT package.
See the provided ReadMe for more information.
To contact the author, e-mail:
Help
Please see the manual(s) and ReadMe distributed with the program for details on program options etc. If all else fails, please contact me.
Citing COMPARIMOTIF
When publishing analyses performed with this software,
please cite:
- Davey NE, Edwards RJ, Shields DC (2007): The SLiMDisc server: short, linear motif discovery in proteins.Nucleic Acids Res. 35(Web Server issue):W455-9.
RJ Edwards (2009). Last modified 04th Sep 2009.