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

[Robert Gentleman]

Hi,
   It is in general a bad idea to rewrite something in a different  
language, unless there are good reasons. The interoperability of R, and  
other languages, like Perl and Python makes it possible to often reuse  
rather than reinvent. That said, the complexity involved is not trivial  
and many find it hard to manage keeping the systems in snyc. I find  
that if I want to do anything more - in terms of analysis or  
visualization then I am going to need to get the data over to R, so it  
tends to be involved in any event.

    We wrote the Biostrings package in part to better understand the  
algorithms from Gusfield's book and in part because for a digital  
karyotyping project that we were working on we found that the available  
perl solutions were too slow. For some of the pattern matching  
Biostrings was much faster - your mileage may vary. It too is not  
complete - but there is some very nice code there. And there is nice  
code in other places - reuse beats reinvention.

Robert

ps the folks that wrote seqinR seem to be confused about the name  
though - from CRAN you need to download seqinr, also note it does not  
seem to handle the extended DNA alphabet - which is something I find I  
need if I'm doing very much sequence work


On May 18, 2005, at 4:32 AM, Aedin 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
>
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
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