Re: C language and bioinformatics

Hi,
Perl is the preffered language for basic bioinformatics programng, say
seqeuence (manipulation) and structure analysis is much more easier in perl
than in any other language. Now a days python is also favoured by
computational biologists looking in to the sequence data.
We have lots of modules available from Bio* projects

http://bioperl.org
http://biopython.org

thats my 2 cents !!!
--
Shameer Khadar
Bioinformatician frm india
On 1/25/07, zentara <zentara@xxxxxxxxxxxxxx> wrote:

On Wed, 24 Jan 2007 14:45:42 -0600, kviel@xxxxxxxxxxxxxxx (Kevin Viel)
wrote:

>chen li wrote:
>> Hi all,
>>
>> It is off-topic but I just wonder if any one knows a
>> website or books talking about reading/processing DNA
>> sequences with C language.
>
>In short, no. You have not provided much information, i.e. what kind of
>sequences or the nature of the processing, but ABI.pm is available on
>CPAN. I have been writing a suite in SAS (sorry perl-people), to
>compare a series of *.ab1 files to a reference sequence to look for
>genetic variables. That is simply accomplished in perl. Visually
>discrepancies is beyond me.
>
>Given the imminence of megabase and whole genome resequencing (3 billion
>data points per subject X 3 bits minimum), you can bet that such a suite
>will be the standard; noone is going to expect a technician to review
>the data.
>Kevin

Hi, this is just a brainstorming idea, but PDL might have some
usefullness here. It uses Fortran behind the scenes, to give
c-like speed to storing and handling huge arrays of data, while
using Perl as a front end to make things easier.

Of course, it's all numbers at that level, so you would have to work
out a scheme for converting back-and-forth, between the gene
text strings and numbers.

PDL is as fast as c, once it gets to the actual number crunching,
and the data storage is very efficient as well.

See:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html




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