[Bioc-devel] New seqPattern package

[Vanja Haberle]

Dear Bioconductor members,

I'd like to draw your attention to the new package for visualisation of 
oligonucleotide patterns and motif occurrences across a set of sorted 
sequences.
The *seqPattern* package is now available in the development branch:
http://www.bioconductor.org/packages/devel/bioc/html/seqPattern.html

This package is designed to visualise sequence patterns across a large 
set of sequences
(/e.g/. promoters, enhancers, ChIPseq peaks, /etc./) centred at a common 
reference position (/e.g./ TSS, peak position) and ordered by some 
feature. The visualisations include plotting the density of occurrences 
of di-, tri-, and in general any oligo-nucleotides, consensus
sequences specified using IUPAC nucleotide ambiguity codes and motifs 
specified by a position weight matrix (PWM). Such visualisations are 
useful in discovering sequence patterns
positionally constrained with respect to the reference point and their 
correlation with the
specified feature.

Your comments and suggestions are welcome and will assist in 
continuously improving the package.

Kind regards,

Vanja

-- 
Vanja Haberle, PhD
Postdoctoral Training Scientist
Computational Regulatory Genomics Group
MRC Clinical Sciences Centre

Hammersmith Hospital Campus
Du Cane Road
London W12 0NN, UK

vanja.haberle at csc.mrc.ac.uk



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