SITE VISIT: MolyBio Toolkit

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Science  10 Jul 1998:
Vol. 281, Issue 5374, pp. 139
DOI: 10.1126/science.281.5374.139b

Molecular biologists spend large chunks of their lives breaking up cells, extracting proteins and DNA, and running the stuff through gels and machines. But that's just the half of it—then they've got to go to a computer to make sense of the data, choosing from thousands of software tools. It's not always easy to find the right one, especially for free, on the Internet.

That's why Christopher M. Smith of the San Diego Supercomputer Center created CMS Molecular Biology Resources (www.sdsc.edu/ResTools/cmshp.html), which he describes as a “functional” listing of public-domain bio Web tools. Web sites typically list these tools by name or location, explains Smith, a biochemist turned computational biologist. But he's gone a step further: The 1900 or so links here are organized according to the task at hand, whether it's identifying a protein based on its peptide fragment map, scouring a gene for coding regions, predicting a protein's 3D structure, or doing a phylogenetic analysis.

The site runs down well-known tools like BLAST (Basic Local Alignment Search Tool), which combs databases for similar DNA or protein sequences. But “there are a lot of other useful tools that researchers aren't aware of,” Smith says. One called WebCutter, for example, allows you to predict how many fragments you'd get if you cut up a nucleotide sequence with enzymes—without ever setting foot in a lab.

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