User: Cabbagesofdoom

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Evolutionary (computational) biologist, writer of open-source bioinformatics software, coffee lover, cat servant and general geek.

Posts by Cabbagesofdoom

<prev • 15 results • page 2 of 2 • next >
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Answer: A: Strategizing Blast Result Parsing
... Do you have redundancy in both query and search sets of sequences? And are you trying to remove redundancy from both from the output? You want to make sure that you are also handling partially overlapping hits where one might be longer at the start and the other at the end - presumably you would wan ...
written 5.4 years ago by Cabbagesofdoom110
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Comment: C: What Tools Are There For Making Regular Expression Motifs From Aligned Sequences
... 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.) ...
written 5.4 years ago by Cabbagesofdoom110
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Comment: C: What Tools Are There For Making Regular Expression Motifs From Aligned Sequences
... 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 ...
written 5.4 years ago by Cabbagesofdoom110
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What Tools Are There For Making Regular Expression Motifs From Aligned Sequences?
... 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 ...
motif protein written 5.4 years ago by Cabbagesofdoom110 • updated 5.4 years ago by Zev.Kronenberg11k
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Answer: A: Scoring The Results From Different Motif Discovery Software
... The answer to the question "which software did better?" depends very much on what you are hoping to achieve. Is this a benchmarking study, in which you know the motifs you are looking for, or is this a motif discovery project? If the former, then the standard method is some kind of sensitivity (TP/ ...
written 5.8 years ago by Cabbagesofdoom110

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For What Tools Are There For Making Regular Expression Motifs From Aligned Sequences?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: The Organisation Of Really Contrived Acronyms (Orca)
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