title: Efficient decoding algorithms for generalized hidden Markov model gene finders.
abstract: BACKGROUND
  The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity.
  
  
  RESULTS
  As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN.
  
  
  CONCLUSIONS
  In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques.
authors.affiliation: Bioinformatics Department, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, USA. bmajoros@tigr.org
authors.forename: William H
authors.initials: WH
authors.lastname: Majoros
authors.forename: Mihaela
authors.initials: M
authors.lastname: Pertea
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome; D015894:Genome, Human; D006801:Humans; D016013:Likelihood Functions; D008390:Markov Chains; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D011336:Probability; D011381:Programming Languages; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004247:DNA