[BioC] PairwiseAlignedXStringSet from pre-aligned sequence

Hervé Pagès hpages at fhcrc.org
Fri Mar 4 23:18:16 CET 2011

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.


> Best,
> Jonathan
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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