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Nucleic Acids Research 2005 33(Web Server Issue):W770-W773; doi:10.1093/nar/gki432
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Current Comparative Table (CCT) automates customized searches of dynamic biological databases

Benjamin R. Landsteiner, Michael R. Olson and Robert Rutherford*

Department of Biology, St Olaf College 1520 St Olaf Avenue, Northfield, MN 55057, USA

*To whom correspondence should be addressed. Tel: +1 507 646 3804; Fax: +1 507 646 3968; Email: robruth{at}stolaf.edu

Received February 14, 2005. Revised March 24, 2005. Accepted March 24, 2005.

The Current Comparative Table (CCT) software program enables working biologists to automate customized bioinformatics searches, typically of remote sequence or HMM (hidden Markov model) databases. CCT currently supports BLAST, hmmpfam and other programs useful for gene and ortholog identification. The software is web based, has a BioPerl core and can be used remotely via a browser or locally on Mac OS X or Linux machines. CCT is particularly useful to scientists who study large sets of molecules in today's evolving information landscape because it color-codes all result files by age and highlights even tiny changes in sequence or annotation. By empowering non-bioinformaticians to automate custom searches and examine current results in context at a glance, CCT allows a remote database submission in the evening to influence the next morning's bench experiment. A demonstration of CCT is available at http://orb.public.stolaf.edu/CCTdemo and the open source software is freely available from http://sourceforge.net/projects/orb-cct.


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