Hi, There are some O'Reilly books on the topic of Perl and Bioinformatics as well. I haven't read them.
http://www.oreilly.com/catalog/begperlbio/ http://www.oreilly.com/catalog/mperlbio/ Cheers, Mike On 2/3/07, I BioKid <[EMAIL PROTECTED]> wrote:
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 <[EMAIL PROTECTED]> wrote: > > On Wed, 24 Jan 2007 14:45:42 -0600, [EMAIL PROTECTED] (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 > > > > > -- > I'm not really a human, but I play one on earth. > http://zentara.net/japh.html > > -- > To unsubscribe, e-mail: [EMAIL PROTECTED] > For additional commands, e-mail: [EMAIL PROTECTED] > http://learn.perl.org/ > > >
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