Which is the best tool available on the web for predicting genes from DNA sequences, and why?
Answers:
You are not very specific about what you want to do, do you have a sequence you want to translate? Or are you looking for different open reading frames in a sequence? Or are you looking at sequence homology.
I'm a big fan of the ExPASY site, it has lots of links and so on. You can do your BLAST searches to look for sequence homologies, use the translate and reverse translate tools for looking at different open reading frames and it has all the proteomics databases on there as well.
http://tw.expasy.org/
I've also added the site for the NCBI BLAST search.
http://www.ncbi.nlm.nih.gov/blast/.
There is an open source package called bioconductor available for R, the statistical computing language. Combined together, it should do anything you want and even more.
www.bioconductor.org
www.r-project.org/
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