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 [[alternative HTML version deleted]]

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 > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi, We are currently under development a package to visualize the sequence-motif. Maybe you could help you in your analyze. Best Regards Arnaud. On 27/08/09 11:17 AM, "Glazko, Galina" <galina_glazko at="" urmc.rochester.edu=""> wrote: 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor