title: A novel hybrid gene prediction method employing protein multiple sequence alignments.
abstract: BACKGROUND
  As improved DNA sequencing techniques have increased enormously the speed of producing new eukaryotic genome assemblies, the further development of automated gene prediction methods continues to be essential. While the classification of proteins into families is a task heavily relying on correct gene predictions, it can at the same time provide a source of additional information for the prediction, complementary to those presently used.
  
  
  RESULTS
  We extended the gene prediction software AUGUSTUS by a method that employs block profiles generated from multiple sequence alignments as a protein signature to improve the accuracy of the prediction. Equipped with profiles modelling human dynein heavy chain (DHC) proteins and other families, AUGUSTUS was run on the genomic sequences known to contain members of these families. Compared with AUGUSTUS' ab initio version, the rate of genes predicted with high accuracy showed a dramatic increase.
  
  
  BACKGROUND
  The AUGUSTUS project web page is located at http://augustus.gobics.de, with the executable program as well as the source code available for download.
authors.affiliation: Institute of Computer Science, University of Göttingen, Goldschmidtstrasse 7, Greifswald, Germany. keller@cs.uni-goettingen.de
authors.forename: Oliver
authors.initials: O
authors.lastname: Keller
authors.forename: Martin
authors.initials: M
authors.lastname: Kollmar
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
authors.forename: Stephan
authors.initials: S
authors.lastname: Waack
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods; D004398:Dyneins / Q000235:genetics; D001330:Electronic Data Processing / Q000379:methods*; D005091:Exons; D006801:Humans; D008957:Models, Genetic; D005810:Multigene Family; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D004398:Dyneins