TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders

By William H. Majoros, Mihaela Pertea, Steven L. Salzberg. Bioinform., 2004

1,755 citations recorded by the source corpus.

Subfields: Epidemiology, Molecular Biology, Parasitology

View Paper: https://www.semanticscholar.org/paper/64540534df8e756e3f8128763ea33aba5c00cc69

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Epidemiology

1. Mario Stanke
2. Burkhard Morgenstern
3. A. Tzvetkova

In Molecular Biology

1. Steven L. Salzberg
2. Mario Stanke
3. Burkhard Morgenstern
4. A. Tzvetkova
5. Arthur L. Delcher
6. Brian J. Haas
7. Mihaela Pertea
8. Jonathan A. Eisen

In Parasitology

1. Mario Stanke
2. Burkhard Morgenstern
3. A. Tzvetkova
4. P. Keeling
5. N. Corradi

Citations in the corpus

• Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, methodology): “The ab initio gene prediction programs Fgenesh [5], Gene-Mark.hmm [6], and GlimmerHMM [4] were applied to the rice genome sequences.”
• Development of Genetic and Genomic Research Resources for Brachypodium distachyon, a New Model System for Grass Crop Research (2008, positive): “Th us, ab initio gene-fi nding algorithms (Lukashin and Borodovsky, 1998; Salamov and Solovyev, 2000; Korf et al., 2001; Majoros et al., 2004) will be used to predict gene models.”
• Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, methodology): “The ab initio gene prediction was conducted by combining the results of three programs, GeneMark.hmm (Lukashin and Borodovsky 1998), GeneZilla (Majoros et al. 2005) and GlimmerHMM (Majoros et al. 2004), using JIGSAW (Allen and Salzberg 2005).”
• Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation (2008, positive): “GlimmerHMM, and fgenesh gene-prediction programs as described in the “Materials and methods” section (Burge and Karlin 1997; Salamov and Solovyev 2000; Majoros et al. 2004; Besemer and Borodovsky 2005).”
• EGASP: the human ENCODE Genome Annotation Assessment Project (2006, background): “2 GENEMARK.hmm Georgia Institute of Technology [60] 2 GENEZILLA TIGR [ 81 ]”