Tuesday, 21 August 2012

CompariMotif V3.6

Both the webserver and SLiMSuite download have now been updated to CompariMotif Version 3.6.

One of the main changes over earlier versions of CompariMotif is that ELM Class exports can now be used directly as input. Any tab-delimited file (*.tdt or *.tsv) with a "Regex" field header will be recognised and motifs extracted using the ELMIdentifier, Regex and Description fields.

To handle some of the more complex motifs now in ELM, the motif splitting function has also been expanded and strengthened. (The caveat is the small bug in the current download which will be fixed in the next release.) In addition to either/or regex elements, variable length non-wildcards are now recognised and will be reformatted for CompariMotif searching.

For example:
Motif [IL]{1,2}[^P].(RG|K)
will be split to form:
Motif_a [IL][^P].RG
Motif_b [IL][^P].K
Motif_c [IL][IL][^P].RG
Motif_d [IL][IL][^P].K
The descriptions will also be appended with "Version 1", "Version 2" etc.

The final minor update replaces ? in motif Regex patterns with .{0,1}. As it uses the same modules for motif input, these changes will also affect SLiMSearch input but not (yet) be taken into consideration for the SLiMChance statistics.

Note. The 2008 version of ELM on the bioware server was manually split and therefore the suffixes added by CompariMotif for later versions of ELM will not necessarily match up.

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