January 15, 2013 (Vol. 33, No. 2)


Strong Points: Includes glossary, two different operating modes
Weak Points: No user guide


If you are interested in studying protein domains—their phyletic distributions, functional class, important amino acid residues, etc.—then it would be a “smart” move to visit the website for the Simple Modular Architecture Research Tool (SMART). Originally described in a 1998 publication, this tool is still very actively updated, with the most recent publication related to SMART being published this year. Through its ability to identify modular domains from user-inputted protein sequences or sequence IDs, SMART is a great tool for scientists interested in the analysis of protein domain architecture. SMART can be used in two modes: normal or genomic. Whereas the normal mode includes various proteome sources in its database, the genomic mode only includes the proteomes of completely sequenced genomes. The site includes a glossary to familiarize users with some of the jargon they might encounter when using SMART, such as “HMM consensus” and “seed alignment.”

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