title: Exploration of multivariate analysis in microbial coding sequence modeling.
abstract: BACKGROUND
  Gene finding is a complicated procedure that encapsulates algorithms for coding sequence modeling, identification of promoter regions, issues concerning overlapping genes and more. In the present study we focus on coding sequence modeling algorithms; that is, algorithms for identification and prediction of the actual coding sequences from genomic DNA. In this respect, we promote a novel multivariate method known as Canonical Powered Partial Least Squares (CPPLS) as an alternative to the commonly used Interpolated Markov model (IMM). Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties.
  
  
  RESULTS
  The multivariate CPPLS approach classified coding sequence substantially better than the commonly used IMM on the same set of sequences. We also found that the use of CPPLS with codon representation gave significantly better classification results than both IMM with protein (p < 0.001) and with DNA (p < 0.001). Further, although the mean performance was similar, the variation of CPPLS performance on codon representation was significantly smaller than for IMM (p < 0.001).
  
  
  CONCLUSIONS
  The performance of coding sequence modeling can be substantially improved by using an algorithm based on the multivariate CPPLS method applied to codon or DNA frequencies.
authors.affiliation: Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway. tahir.mehmood@umb.no
authors.forename: Tahir
authors.initials: T
authors.lastname: Mehmood
authors.forename: Jon
authors.initials: J
authors.lastname: Bohlin
authors.forename: Anja Bråthen
authors.initials: AB
authors.lastname: Kristoffersen
authors.forename: Solve
authors.initials: S
authors.lastname: Sæbø
authors.forename: Jonas
authors.initials: J
authors.lastname: Warringer
authors.forename: Lars
authors.initials: L
authors.lastname: Snipen
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D003062:Codon; D005807:Genes, Overlapping; D023281:Genomics; D008390:Markov Chains; D008957:Models, Genetic; D015999:Multivariate Analysis; D016366:Open Reading Frames; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
chemical_list: D003062:Codon