Question: What Tools Are There For Making Regular Expression Motifs From Aligned Sequences?
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gravatar for Cabbagesofdoom
5.4 years ago by
Southampton
Cabbagesofdoom110 wrote:

I recently knocked together a little tool, SLiMMaker, for generating regular expressions from protein sequences (http://bioware.soton.ac.uk/slimmaker.html). It wouldn't be too hard to knock together some proper documentation for it but, before doing so, I was wondering whether anyone (a) thought it might be useful, and/or (b) knows of an existing tool elsewhere that already does the same job?

(Edit to clarify: this is not a motif-hunting application, like MEME, SLiMFinder, DILIMOT etc., it is a simple application that tries to build the best regular expression according to certain user-constraints (max amount of degeneracy, min aa frequency, min coverage) from already aligned short sequences. It was actually designed for taking a set of instances from the ELM database and redefining the motif based on those sequences alone - ELM incorporates a lot of experimental evidence that is not always represented by the known biological occurrences.)

motif protein • 2.0k views
ADD COMMENTlink modified 5.4 years ago by Zev.Kronenberg11k • written 5.4 years ago by Cabbagesofdoom110

amusingly just a few days ago I posted about this tool in tools section - I will reclassify your post as a tool and delete mine

ADD REPLYlink written 5.4 years ago by Istvan Albert ♦♦ 73k

Thanks. Your tools post is more informative, though, and I really just want feedback about similar things around, so I'd prefer this as a question and your tools post to remain. (I've not posted much here, though, so that might constitute inappropriate doubling up, rather than adding clarity.) I've changed it back to a question for now but can add more information and change it back if you think it is better to have a single tools/question post!

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Cabbagesofdoom110

sure no problem, I would change the title to be a question then, something like: Are there other tools similar to SLiMMaker?

ADD REPLYlink written 5.4 years ago by Istvan Albert ♦♦ 73k
0
gravatar for Zev.Kronenberg
5.4 years ago by
United States
Zev.Kronenberg11k wrote:

The MEME suite can do all sorts of motif matching.

ADD COMMENTlink written 5.4 years ago by Zev.Kronenberg11k

It can but I am not aware of any tool in MEME Suite for converting a set of short sequences into a single regular expression according to certain constraints. (This is not really a motif-hunting problem.)

ADD REPLYlink written 5.4 years ago by Cabbagesofdoom110
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