title: Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes.
abstract: BACKGROUND
  Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently, labour-intensive manual curation is often necessary. We present Figmop (Finding Genes using Motif Patterns) to help with the manual curation of gene families in draft genome assemblies. The program uses a pattern of short sequence motifs to identify putative genes directly from the genome sequence. Using a large gene family as a test case, Figmop was found to be more sensitive and specific than a BLAST-based approach. The visualization used allows the validation of potential genes to be carried out quickly and easily, saving hours if not days from an analysis.
  
  
  METHODS
  Source code of Figmop is freely available for download at https://github.com/dave-the-scientist, implemented in C and Python and is supported on Linux, Unix and MacOSX.
  
  
  BACKGROUND
  curran.dave.m@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Ecosystem and Public Health and Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada Department of Ecosystem and Public Health and Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada.
authors.forename: David M
authors.initials: DM
authors.lastname: Curran
authors.affiliation: Department of Ecosystem and Public Health and Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada.
authors.forename: John S
authors.initials: JS
authors.lastname: Gilleard
authors.affiliation: Department of Ecosystem and Public Health and Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada.
authors.forename: James D
authors.initials: JD
authors.lastname: Wasmuth
mesh_terms: D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D005796:Genes; D023281:Genomics / Q000379:methods*; D008390:Markov Chains; D008957:Models, Genetic; D005810:Multigene Family; D012984:Software
chemical_list: D003577:Cytochrome P-450 Enzyme System