title: Finding novel genes in bacterial communities isolated from the environment.
abstract: BACKGROUND
  Novel sequencing techniques can give access to organisms that are difficult to cultivate using conventional methods. When applied to environmental samples, the data generated has some drawbacks, e.g. short length of assembled contigs, in-frame stop codons and frame shifts. Unfortunately, current gene finders cannot circumvent these difficulties. At the same time, the automated prediction of genes is a prerequisite for the increasing amount of genomic sequences to ensure progress in metagenomics.
  
  
  RESULTS
  We introduce a novel gene finding algorithm that incorporates features overcoming the short length of the assembled contigs from environmental data, in-frame stop codons as well as frame shifts contained in bacterial sequences. The results show that by searching for sequence similarities in an environmental sample our algorithm is capable of detecting a high fraction of its gene content, depending on the species composition and the overall size of the sample. The method is valuable for hunting novel unknown genes that may be specific for the habitat where the sample is taken. Finally, we show that our algorithm can even exploit the limited information contained in the short reads generated by 454 technology for the prediction of protein coding genes.
  
  
  BACKGROUND
  The program is freely available upon request.
authors.affiliation: Bielefeld University, Center for Biotechnology (CeBiTec), D-33594 Bielefeld, Germany. Lutz.Krause@CeBiTec.Uni-Bielefeld.DE
authors.forename: Lutz
authors.initials: L
authors.lastname: Krause
authors.forename: Naryttza N
authors.initials: NN
authors.lastname: Diaz
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Jens
authors.initials: J
authors.lastname: Stoye
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics*; D004783:Environmental Microbiology; D004784:Environmental Monitoring / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial