Jonathan G Campbell wrote:
>> Go with Java. You'll be at least twice as productive as with C++ or C.
> Of course, if _all_ you are doing (and aiming to do) is ripping text
> files apart and putting them together in another way, then the Perl
> suggestion is apt.
I'd say go for Perl! It excels at manipulating text (biological
sequences) and there is a very useful collection of functions and
objects at www.bioperl.org. With bioperl you can easily interface to
databases and external analysis programs (like BLAST).Most of the hard
(and boring) stuff of parsing files and handling in- and output have
been done for you, so can start asking (and answering) the interesting
biological questions.
Bioperl is being actively developed by some of the top scientists in
bioinformatics.
And the learning curve is quite shallow, albeit rather long.
It runs easiest under unix (very easy installation for Redhat+Suse at
www.biolinux.org ), but should also work on windows and macs.
good luck,
Morten Lindow
grad student in bioinformatics, Univ. Copenhagen.
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