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Bioinformatics Advance Access originally published online on September 13, 2007
Bioinformatics 2007 23(22):2961-2968; doi:10.1093/bioinformatics/btm421
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Published by Oxford University Press (2007).

Evolutionary analysis of enzymes using Chisel

Alexis A. Rodriguez 1,2,*, Tanuja Bompada 1, Mustafa Syed 1, Parantu K. Shah 3 and Natalia Maltsev 1,2,*

1Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439, 2Computation Institute, The University of Chicago, 5640 S. Ellis Avenue, RI 405, Chicago, IL 60637 and 3Department of Human Genetics, The University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.

Results: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, ‘binning’ of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.

Availability: Chisel is available for interactive use at http://compbio.mcs.anl.gov/CHISEL. The website also provides a user manual, clusters and function-specific computational models.

Contact: arodri7{at}mcs.anl.gov or maltsev{at}mcs.anl.gov

Supplementary information: Additional data can be found at http://compbio.mcs.anl.gov/CHISEL/htmls/refs.html

Associate Editor: John Quackenbush

Received on May 25, 2007; revised on July 17, 2007; accepted on August 13, 2007

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