[BioC] sequence-motif visuazation (motifs found with DNAString)

[Michael Dondrup]

Hi,
maybe you can try the seqLogo package

seqLogo
Sequence logos for DNA sequence alignments
seqLogo takes the position weight matrix of a DNA sequence motif and  
plots the corresponding sequence logo as introduced by Schneider and  
Stephens (1990).

that could visualize the motif part when given a PWM at least.

Best

Michael

Am 27.08.2009 um 17:17 schrieb Glazko, Galina:

> Dear all,
>
>
>
> I need an advice: I have a set of sequences together with motifs found
> using DNAString function (Biostrings). Is there a package I can use to
> visualize the matching, to make a picture similar to, e.g.:
>
>
>
>                  Motif:NTTTTTTTCTTTTTTTNNNNNNN
>
> ACGTTGCTATCGTATAAAAAAAAATTTTTTTTCTTTTTTTTTTTTTT
>
>                        -60
>
> Thank you!
>
> Best regards
>
> Galina
>
>
>
>
>
>
>
>
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