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]]

