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.habe...@csc.mrc.ac.uk [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel