Efficient decoding algorithms for generalized hidden Markov model gene finders

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Majoros, William H ^a   Pertea, Mihaela ^a   Delcher, Arthur L ^a   Salzberg, Steven L ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL COSTS; DECODING ALGORITHM; GENERALIZED HIDDEN MARKOV MODELS; HOMOLOGY INFORMATION; OPEN SOURCE SOFTWARE SYSTEMS; OPTIMIZED ALGORITHMS; PREDICTION ACCURACY; PREDICTION PROCESS;

ALGORITHMS; COMPUTATIONAL EFFICIENCY; FORECASTING; HIDDEN MARKOV MODELS; OPTIMIZATION;

GENES;

ACCURACY; ARTICLE; COMPUTER PROGRAM; COST BENEFIT ANALYSIS; DNA SEQUENCE; EUKARYOTE; FEASIBILITY STUDY; GENE EXPRESSION; GENETIC ALGORITHM; GENETIC CODE; GENOME; MATHEMATICAL COMPUTING; PREDICTION; PROBABILITY; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; ALGORITHM; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER LANGUAGE; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; HUMAN; HUMAN GENOME; PROCEDURES; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

EUKARYOTA;

DNA;

ALGORITHMS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, GENETIC; DNA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME; GENOME, HUMAN; HUMANS; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, BIOLOGICAL; MODELS, GENETIC; MODELS, STATISTICAL; PROBABILITY; PROGRAMMING LANGUAGES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 13244265565     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-6-16     Document Type: Article

References (14)

1. Kulp D, Haussler D, Reese MG, Eeckman FH: A generalized hidden Markov model for the recognition of human genes in DNA. In: Proceedings of the fourth International Conference on Intelligent Systems for Molecular Biology 1996:134-142.
2. Burge C: Identification of Genes in Human Genomic DNA. PhD Thesis. Department of Mathematics, Stanford University; 1997.
3. Cawley SE, Wirth AI, Speed TP: Phat - a gene finding program for Plasmodium falciparum. Mol & Biochem Parasitology 118, 2001:167-174.
4. Stanke M, Waack S: Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, 2003:II215-II225.
5. Majoros WM, Pertea M, Salzberg SL: TIGRscan and GlimmerHMM: two open-source ab initio eukaryotic gene finders. Bioinformatics 20, 2004:2878-2879.
6. Korf I: Gene finding in novel genomes. BMC Bioinf 5, 2004:59.
7. Pachter L, Alexandersson M, Cawley S: Applications of generalized pair hidden Markov models to alignment and gene finding problems. J Comput Biol 9, 2002:389-399.
8. Alexandersson M, Cawley S, Pachter L: SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res 13, 2003:496-502.
9. Rabiner LR, Juang B-H: An introduction to hidden Markov models. IEEE Transactions on Acoustics Speech, Signal Processing 3, 1986:4-16.
10. Rabiner LR: A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 1989:257-286.
11. Salzberg SL, Searls DB, Kasif S: Computational Methods in Molecular Biology. Amsterdam: Elsevier; 1998.
12. Durbin R, Eddy S, Krogh A, Mitchison G: Biological Sequence Analysis. Cambridge University Press; 1998.
13. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 268, 1997:78-94.
14. Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H: Interpolated Markov models for eukaryotic gene finding. Genomics 59, 1999:24-31.