C programming in bioinformatics - (May/24/2007 )

Hi everyone,

I've been heavily using Perl and Python for sometime now and am very interested in learning C. I'm even taking a class next semester to pursue such an interest.
But after searching forums and talking to profs, I get the impression that C programming is mainly used in algorithm design, HMM, tree analysis and other computationally intensive activities. I'm curious how C can be used in bio-computing in ways that Perl or Python cannot.
I'd be appreciative if anyones' worked with C in bioinformatics. Thanks in advance,

hi,
i take one course in C, and try to practice what i already know on DNA mainpulation (transcription and so on), but i'm not expert though

Hello,

I think that you will tend to use certain languages for specific tasks. Day to day I use perl and python (sometimes bash and c-shell) to get tasks done, this includes text manipulation, file operations and sorting small datasets. For more computationally intensive tasks c/c++ and java are far better - the time taken to execute a program in C/C++ will be much shorter than perl - one of my perl scripts runs about 7-9 secs in perl and under 1 in c++.

I would suggest that you learn one of perl/python AND java/C++. I think most people in this lab know two, those that don't know the hard-core languages such as C and fortran and can muster up some hefty code.

The great thing about C and other OO languages is that the code is far easier to maintain - something I find myself having problems with when it comes to my perl scripts.

Really it is ALL ABOUT THE SPEED... if you want fast execution time use c++, if you want fast coding use perl.

HTH