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

[fhong at salk.edu]

Hi Aedin;

Thank you for your reply.

> 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?
There are some algorithm which was originally implemented in other
environment, but has been re-written in R later due to the popularity of
the usage of R.
In stead of spending time learning (there is still a decent percentage of
R users that don't know Perl well), I think maybe most user prefer to have
it written in R, even an less perfect version. One can always go to those
better-written algorithm later if there is a need.

Well, this is just my personal opinion.

Fangxin





> Regards,
> Aedin
>
>
>
>
>
>
>


--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105