[BioC] Re: Sequence alignment for DNA sequences (John Zhang)

[A.J. Rossini]

Sure, and MEGA is a wonderful alignment tool, though last time I used
it, 3+ years ago, it wasn't scriptable.

I'd prefer reuse rather than reinvention, but there is a good deal to
be gained from leveraging some of the statistically oriented tools
(and overall systems biology integration that is happening in R).

With respect to RSperl, we'd have to write data converters.  Might be
possible, but the right approach would be to start with the BioStrings
package and flesh it out for activities.

A fun activity, but unfortunately far removed from my current day job.

best,
-tony

On 5/18/05, Aedin <Aedin.Culhane at ucd.ie> wrote:
> Hi
> Might also be useful to look at some of the functions in seqinR.
> 
> Sorry about this, but can I ask an off topic question?  Many nucleotide
> alignment algorithms are available. Are we replicating the effort of
> programs like Bioperl/EMBOSS etc etc in R?  What are people's experience
> with RSperl and other "connectivity" modules?
> 
> Regards,
> Aedin
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 


-- 
best,
-tony

"Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes" (AJR, 4Jan05).

A.J. Rossini
blindglobe at gmail.com