CompariMotif Help Pages

Pages:

• Bioware Home

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• CompariMotif Manual - (PDF)
• Download & Readme

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• Main CompariMotif Help

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• Input
• Options
• Output

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• How CompariMotif works
• CompariMotif Relationships
• Example Application

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• SLiM Databases
• References and Citations

CompariMotif Input

CompariMotif takes either one or two motif lists as input. If only one list is given, motifs from this list will be compared with themselves. Motifs can either be pasted into the text box, uploaded into the file browser box, or selected from the drop-down list of pre-defined motif datasets. Datasets available include:

• Motifs from the ELM database of eukaryotic SLiMs. Note that some motifs have been split into _a and _b to be compatible with CompariMotif input formats. Such motifs are marked *Modified* in their descriptions.
• Motifs from the MiniMotif 1.0 database of SLiMs. These motifs have been reformatted to conform to standard regular expressions.
• Motifs from the PhosphoMotif Finder database of HPRD. Note that all these motifs are phosphorylation motifs and, as such, have a key Ser, Thr or Tyr position. These are not given special treatment in CompariMotif and the user should pay special attention to whether the appropriate residue is included in the match.
• Miscellaneous motifs collected from the literature. (These include pubmed links to the relevant paper but we cannot guarantee the accuracy of the motifs or their descriptions.)
• A combined database of the above sources. The source database is indicated in the motif description: [ELM] for ELM, [MnM] for MiniMotif and [PMF] for PhosphoMotif Finder.
• Predicted interaction SLiMs from the high-throughput study of Neduva et al. (2005).

When using results from any of these databases, please cite the appropriate papers. Suggested citations and fuller descriptions of the contents of these files can be found here or in the CompariMotif Manual.

For full details of acceptable input formats, please see the CompariMotif Manual.

Note. If CompariMotif is being run directly from the SLiMDisc webserver, these input options are only presented for the search database. The primary input will always be the top 20 SLiMDisc motifs.

Example Input

These examples correspond to the motifs returned by SLiMFinder in the Example Application. Recomended format is: <Name Pattern # Description> where Name and Pattern have no whitespace:

# Anything following a "#" is ignored as a comment
YWHAE_1  R..S.P..L       # Significant motif from SLiMFinder analysis of 14-3-3 Epsilon interactors from HPRD
YWHAH_1  GR.[ST]..P      # Significant motif from SLiMFinder analysis of 14-3-3 Eta interactors from HPRD
YHWAG_1  ^.[AS][AGS]     # Significant motif from SLiMFinder analysis of 14-3-3 Gamma interactors from HPRD
YHWAG_2  KE..K           # Significant motif from SLiMFinder analysis of 14-3-3 Gamma interactors from HPRD
YWHAQ_1  P..P..P         # Significant motif from SLiMFinder analysis of 14-3-3 Theta interactors from HPRD
YWHAZ_1  [AGS]..P..P..P  # Significant motif from SLiMFinder analysis of 14-3-3 Zeta interactors from HPRD
YWHAZ_2  ^.[AGS][GS]     # Significant motif from SLiMFinder analysis of 14-3-3 Zeta interactors from HPRD
YWHAZ_3  FR..[ST].S      # Significant motif from SLiMFinder analysis of 14-3-3 Zeta interactors from HPRD
YWHAZ_4  [ST]P.[ST]P     # Significant motif from SLiMFinder analysis of 14-3-3 Zeta interactors from HPRD
YWHAZ_5  Y.C.PG.L        # Significant motif from SLiMFinder analysis of 14-3-3 Zeta interactors from HPRD

A simpler format is simply a list of motifs. The input above in this format would simply be:

R..S.P..L
GR.[ST]..P
^.[AS][AGS]
KE..K
P..P..P
[AGS]..P..P..P
^.[AGS][GS]
FR..[ST].S
[ST]P.[ST]P
Y.C.PG.L