title: ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.
abstract: BACKGROUND
  The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins.
  
  
  RESULTS
  Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far.
  
  
  CONCLUSIONS
  Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.
authors.affiliation: The Protein Chemistry Group, Institute for Medical Biochemistry, Centre for Biomedical Education and Research, School of Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Str. 10, Witten 58448, Germany.
authors.forename: Arno
authors.initials: A
authors.lastname: Meiler
authors.forename: Claudia
authors.initials: C
authors.lastname: Klinger
authors.forename: Michael
authors.initials: M
authors.lastname: Kaufmann
mesh_terms: D000596:Amino Acids / Q000032:analysis; D001105:Archaea / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics; D001482:Base Composition; D003062:Codon; D030562:Databases, Protein; D009711:Nucleotides / Q000032:analysis; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D017421:Sequence Analysis; D012984:Software; D013696:Temperature
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D003062:Codon; D009711:Nucleotides; D011506:Proteins