Current development for the Bio.Motif module.

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

• which would extend highly extend usability of the Bio.Motif module:

• Writing different implementations for different motif types:
  • consensus sequences (possibly with ambiguity)
  • alignments (gapped or ungapped pwms)
  • motifs with variable-length gaps
• writing conversions from alignments to motif instances (possibly different for different motifs)
• integrating with Bio.Seq and Bio.Align, so that the API is more natural for the end users
• making modifications to Seq.startwswith, .endswith, .find and .rfind to 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.