title: Evolutionary analysis of enzymes using Chisel.
abstract: BACKGROUND
  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.
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439, USA.
authors.forename: Alexis A
authors.initials: AA
authors.lastname: Rodriguez
authors.forename: Tanuja
authors.initials: T
authors.lastname: Bompada
authors.forename: Mustafa
authors.initials: M
authors.lastname: Syed
authors.forename: Parantu K
authors.initials: PK
authors.lastname: Shah
authors.forename: Natalia
authors.initials: N
authors.lastname: Maltsev
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods; D004798:Enzymes / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004798:Enzymes