Hi Herve, Thanks for your response. I have a set of Solid consensus genomes that have been assembled with a reference sequence (therefore they are pre- aligned). The sequences are long (> 25 Mb for each pseudomolecule/contig) and ungapped (ie aligned), so I was hoping to use Biostrings methods that operate on alignment objects. I will look into read.DNAMultipleAlignment(), but it is not clear in the documentation if this class inherits from PairwiseAlignedXStringSet, but if it doesn't then the pairwise string comparison methods I was interested in using likely won't work. Anyhow, thanks for your reply. Best, 2011/3/4 Hervé Pagès <hpages@fhcrc.org> > Hi Jonathan, > > > On 03/01/2011 06:49 PM, Jonathan Flowers wrote: > >> Hello, >> >> I have a set of pre-aligned DNA sequences and would like to create >> AlignedXStringSet or PairwiseAlignedXStringSet objects for use with >> alignment utilities (without running pairwiseAlign). Any assistance would >> be much appreciated. >> > > Unfortunately I don't think there is an easy way to create > AlignedXStringSet or PairwiseAlignedXStringSet objects without > running pairwiseAlignments(). There are no I/O tools in Biostrings > for loading pre-aligned DNA sequences in AlignedXStringSet or > PairwiseAlignedXStringSet objects. > > That being said, there are tools in other packages for loading > pre-aligned DNA sequences into other types of containers. It all > depends what kind of "pre-aligned DNA sequences" you have and how > they are stored. If they are short reads, then you should look at > the I/O tools in the ShortRead package (readAligned() function, > supports many file formats) and also at the readGappedAlignments() > function in the GenomicRanges package (supports BAM files only). > There is even a read.DNAMultipleAlignment() function in Biostrings > for loading the result of a "multiple sequence alignment" (supports > fasta, stockholm and clustal formats). > > Hope this helps. > > Cheers, > H. > > >> Best, >> >> Jonathan >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]