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Current development for the Bio.Motif module. |
wiki/MotifDev |
wiki |
This page describes current state of the development of the
Bio.motifs (formerly Bio.Motif) module.
Enhancements currently underway:
- Expanding the Bio.Motif tutorial on analysis of protein motifs (Dave Bridges is workin on this, see http://github.com/davebridges/biopython-biomotif-supplement/tree/master his branch on github
- writing a simplistic, pure-python, de-novo motif finder
- writing a wrapper for RSAT tools (http://rsat.ulb.ac.be/rsat/) using either local binaries or SOAP
There are also multiple features - suggested mostly by Leighton Pritchard http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005834.html 1 and http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005811.html 2
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which would extend highly extend usability of the Bio.Motif module:
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Writing different implementations for different motif types:
- consensus sequences (possibly with ambiguity)
- alignments (gapped or ungapped pwms)
- motifs with variable-length gaps
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writing conversions from alignments to motif instances (possibly different for different motifs)
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integrating with
Bio.SeqandBio.Align, so that the API is more natural for the end users -
making modifications to
Seq.startwswith,.endswith,.findand.rfindto support passing motifs to them. See also this commit.
Kind of separate issue (also from Leighton) is to take into account HMM based motif searching:
- Supporting HMM-based motifs (with dependencies between positions)
- particular tools like HMMer
If you want to contribute, please contact bartek@rezolwenta.eu.org or biopython@biopython.org.