[BioC] PairwiseAlignedXStringSet from pre-aligned sequence

[Hervé Pagès]

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 at 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 at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319