Glimmer-HMM

GlimmerHMM is a modular and extensible open source Generalized Hidden Markov Model implementation for ab initio eukaryotic gene prediction. It is re-trainable, re-configurable, and includes probabilistic submodels such as Maximal Dependence Decomposition trees and interpolated Markov models. It has been used to annotate numerous genomes, such as the Aspergillus fumigatus and Toxoplasma gondii.

Topic

Gene structure;Genomics

Detail

  • Operation: Gene prediction;Ab-initio gene prediction

  • Software interface: Command-line user interface

  • Language: C++;C

  • License: Open Source

  • Cost: Free

  • Version name: -

  • Credit: -

  • Input: -

  • Output: -

  • Contact: mpertea@jhu.edu

  • Collection: -

  • Maturity: -

Publications

  • Interpolated Markov models for eukaryotic gene finding
  • Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H. Interpolated Markov models for eukaryotic gene finding. Genomics. 1999 Jul 1;59(1):24-31. doi: 10.1006/geno.1999.5854. PMID: 10395796.
  • https://doi.org/10.1006/geno.1999.5854
  • PMID: 10395796
  • PMC: -
  • Finding genes in Plasmodium falciparum
  • Pertea M, Salzberg SL, Gardner MJ. Finding genes in Plasmodium falciparum. Nature. 2000 Mar 2;404(6773):34; discussion 34-5. doi: 10.1038/35003643. PMID: 10716431.
  • https://doi.org/10.1038/35003643
  • PMID: 10716431
  • PMC: -
  • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
  • Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796-815. doi: 10.1038/35048692. PMID: 11130711.
  • https://doi.org/10.1038/35048692
  • PMID: 11130711
  • PMC: -
  • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
  • Majoros WH, et al. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. 2004; 20:2878-9. doi: 10.1093/bioinformatics/bth315
  • https://doi.org/10.1093/bioinformatics/bth315
  • PMID: 15145805
  • PMC: -
  • Computational gene finding in plants
  • Pertea M, Salzberg SL. Computational gene finding in plants. Plant Mol Biol. 2002 Jan;48(1-2):39-48. PMID: 11860211.
  • https://doi.org/keep-11860211
  • PMID: 11860211
  • PMC: -

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