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LETTER: Genome Annotation Assessment in Drosophila melanogaster
- Martin G. Reese,
- George Hartzell,
- Nomi L. Harris,
- Uwe Ohler,
- Josep F. Abril,
- and Suzanna E. Lewis
Genome Res. April 1, 2000 10: 483-501; doi:10.1101/gr.10.4.483
.... Of these 222 gene structures, 182 are similar to a homologous protein in another organism or have a Drosophila EST hit. For these structures, the intron–exon boundaries were verified by partial cDNA/EST alignments using sim4 ( Florea et al. 1998 ), homologies were discovered using BLASTX , TBLASTX , and PFAM...
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LETTER: Evaluation of Gene-Finding Programs on Mammalian Sequences
- Sanja Rogic,
- Alan K. Mackworth,
- and Francis B.F. Ouellette
Genome Res. May 1, 2001 11: 817-832; doi:10.1101/gr.147901
...of British Columbia, Vancouver, BC V6T 1Z4, Canada; 3Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada Abstract We present an independent comparative analysis of seven recently developed gene-finding programs: FGENES , GeneMark.hmm , Genie , Genscan , HMMgene , Morgan , and MZEF...
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LETTER: Computational Inference of Homologous Gene Structures in the Human Genome
- Ru-Fang Yeh,
- Lee P. Lim,
- and Christopher B. Burge
Genome Res. May 1, 2001 11: 803-816; doi:10.1101/gr.175701
...or contaminating genomic DNA ( Wolfsberg and Landsman 1997 ), causing problems for automated gene prediction methods. For example, Krogh (2000) found that the incorporation of EST matches into the sophisticated HMMGene algorithm resulted in lower overall accuracy, with increases in sensitivity more than offset...
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METHODS: GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming
- Kevin L. Howe,
- Tom Chothia,
- and Richard Durbin
Genome Res. September 1, 2002 12: 1418-1427; doi:10.1101/gr.149502
.... ( 1997 ) Two methods for improving performance of a HMM and their application for gene finding. Proc. Intell. Syst. Mol. Biol. 5 : 179 – 186 . ↵ Krogh A. ( 2000 ) Using database matches with HMMGene for automated gene detection on Drosophila. Genome Res. 10 : 523 – 528 . ↵ Kulp D. , Haussler D. , Reese M...
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Methods: EGPred: Prediction of Eukaryotic Genes Using Ab Initio Methods After Combining With Sequence Similarity Approaches
- Biju Issac and
- Gajendra Pal Singh Raghava
Genome Res. September 2004 14: 1756-1766; doi:10.1101/gr.2524704
...). They reported that among the evaluated programs, Genscan ( http://genes.mit.edu/GENSCAN.html ; Burge and Karlin 1997 ) and HMMgene ( http://www.cbs.dtu.dk/services/HMMgene/ ; Krogh 1997 ) were able to predict the precise locations of 70%-80% of the coding exons with low false positives ( Rogic et al. 2001...
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METHODS: A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences
- Trees-Juen Chuang,
- Wen-Chang Lin,
- Hurng-Chun Lee,
- Chi-Wei Wang,
- Keh-Lin Hsiao,
- Zi-Hao Wang,
- Danny Shieh,
- Simon C. Lin,
- and Lan-Yang Ch'ang
Genome Res. February 1, 2003 13: 313-322; doi:10.1101/gr.313703
...–63. Elsevier, Amsterdam. . ↵ ( 2000 ) Using database matches with HMMGene for automated gene detection in Drosophila. Genome Res. 10 : 523 – 528 , ibid . Lander E.S. , Waterman M.S. ( 1995 ) Calculating the secrets of life , Chapter 3. National Academy Press, Washington, DC. . ↵ Lander E.S. , Linton L...
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ENSEMBL Special: GeneWise and Genomewise
- Ewan Birney,
- Michele Clamp,
- and Richard Durbin
Genome Res. May 2004 14: 988-995; doi:10.1101/gr.1865504
.... Initial sequencing and analysis of the human . Nature 409 : 860 -921. ↵ Krogh, A. 2000 . Using database matches with HMMGene for automated gene detection in Drosophila. Genome Res. 10 : 523 -528. ↵ Kulp, D., Haussler, D., Reese, M.G., and Eeckman, F.H. 1996 . A generalized hidden Markov model...

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