[BioC] Biostring: print sequence alignment to file

[Hervé Pagès]

Hi Martin,

On 04/16/2012 04:06 AM, Martin Preusse wrote:
> Hi Charles,
>
> thanks! Your solution allows to print the two alignment strings separately.
>
> I was thinking of an output as generated by alignment tools:
>
> AGT-TCTAT
> | | | |  |  | | | |
> AGTATCTAT

This looks like BLAST output. Is this what you have in mind? Note that
there are many alignment tools and many ways to output the result to a
file. I'm not really familiar with the BLAST output format. Is it
specified somewhere? Would that make sense to add something like a
write.PairwiseAlignedXStringSet() function to Biostrings for writing
the result of pairwiseAlignment() to a file? We could do this and
support the BLAST format if that's a commonly used format.

Thanks,
H.

>
> For this I would have to write a function to output the strings in blocks of e.g. 60 nucleotides, right?
>
> Cheers
> Martin
>
>
>
> Am Freitag, 13. April 2012 um 19:21 schrieb Chu, Charles:
>
>> write.XStringSet
>
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-- 
Hervé Pagès

Program in Computational Biology
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