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CompariMotif help pages
CompariMotif is a simple application for comparing two lists of motifs to identify similar (or identical) motifs.
In the SLiMDisc pipeline, CompariMotif will compare the top 20 motifs returned by SLiMDisc to a local database consisting of ELM,
MiniMotif and some additional SLiMs identified from the literature. Output from CompariMotif is a table of top 20 SLiMDisc motifs
and the known SLiMs they match with the chosen settings. For a full description of CompariMotif functions, please see the main
CompariMotif website and/or download the
full CompariMotif Manual.
By default, the options are quite relaxed and will return a large number of hits. The section below on Output can help
interpret which of these may be interesting.
Here, the main functions relevant to the SLiMDisc webserver are briefly discussed. CompariMotif has only one
output.
Clicking on + View Options should present the following options:
| Server Option
|
Description
|
Commandline Option
|
| Ambiguity cut-off |
The number of different amino acids allowed at one site before it is treated as a wildcard position.
(Otherwise, it will count as one of the positions shared (see minshare, below).) |
ambcut=X |
| Minimum motif length |
Minimum (non-wildcard) length of motifs to consider |
minpep=X |
| Minimum number of shared positions |
Matches between two motifs must share at least this number of non-wildcard positions. |
minshare=X |
| Reverse motifs |
Reverses motifs returned from SLiMDisc. If you get a lot of hits from your SLiMDisc results, this option can give a
sense of how many hits to expect giving the amino acid composition of your results and the CompariMotif settings selected. |
reverse=T/F |
| Must exactly match all fixed positions |
By default, all fixed positions of known SLiMs must match fixed positions in the SLiMDisc motif but fixed positions in
SLiMDisc motifs are allowed to match ambiguous positions in known SLiMs. This option allows the user to alter this restriction to
apply to either, neither or both motifs. |
matchfix=X |
Output of CompariMotif is a sortable text table (see below) for the top 20 motifs returned by SLiMDisc. To analyse different
motifs, use SLiMPickings to return the desired motifs and upload the delimited text file into the standalone
CompariMotif server.
| Output Column
|
Description
|
| Name1 |
This will give the name of the SLiMDisc dataset (SLiMDisc_temp_X, where X is the job ID) followed by #R, where R is the
rank of the motif that has hit a known SLiM. |
| Name2 |
This is the name of the known SLiM that has been hit. This may be an ELM or MiniMotif ID. |
| Motif1 |
The motif definition (pattern) of the SLiMDisc motif. |
| Motif2 |
The motif definition (pattern) of the known SLiM. |
| Similarity1 |
The relationship of the SLiMDisc motif to the known SLiM. (See CompariMotif Relationships below.) |
| Similarity2 |
The relationship of the known SLiM to the SLiMDisc motif. (See CompariMotif Relationships below.) | |
| MatchPos |
The number of matching non-wildcard positions. (This includes positions that match due to ambiguities.)
This must meet the minshare requirement (See options above). |
| MatchIC |
The calculated information content of the match. (See the
CompariMotif Manual for details.) |
| NormIC |
The calculated information content of the match normalised by the maximum possible MatchIC for that pair of motifs.
In essence, higher scores indicate better matches, and a score of 1.0 indicates that no better match was possible between this pair of motifs. (See the
CompariMotif Manual for details.) |
| Info1 |
The information content of the SLiMDisc motif. (Scaled so that 1.0 is the equivalent of 1 fixed position, no gap penalty.) |
| Info2 |
The information content of the known SLiM. (Scaled so that 1.0 is the equivalent of 1 fixed position, no gap penalty.) |
| Desc1 |
The description of the SLiMDisc motif, which is the same as Name1. |
| Desc2 |
The description of the known SLiM. |
The best match for any pair of motifs is considered 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 = the focal motif contains only exact matches and subvariants of degenerate positions compared to 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. (See the
CompariMotif Manual for details.)
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