GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

By John Besemer, Mark Borodovsky. Nucleic Acids Res., 2005

1,146 citations recorded by the source corpus.

The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (). The website provides interfaces to the GeneMark family of programs designed and tuned for gene prediction in prokaryotic, eukaryotic and viral genomic sequences. Currently, the server allows the analysis of nearly 200 prokaryotic and >10 eukaryotic genomes using species-specific versions of the software and pre-computed gene models. In addition, genes in prokaryotic sequences from novel genomes can be identified using models derived on the spot upon sequence submission, either by a relatively simple heuristic approach or by the full-fledged self-training program GeneMarkS. A database of reannotations of >1000 viral genomes by the GeneMarkS program is also available from the web site. The GeneMark website is frequently updated to provide the latest versions of the software and gene models.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2a0423a7435114c6828753eec95ed033ab8f5f11

How researchers see this paper

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

In Ecology

In Molecular Biology

Citations in the corpus

BAGEL: a web-based bacteriocin genome mining tool (2006, methodology): “have been implemented in our ORF tool: (i) Glimmer/ RBSfinder (15); (ii) Zcurve (16) and (iii) GeneMark (17).”
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates (2012, methodology): “6c with a heuristic model, based on the GC content (Besemer and Borodovsky, 2005).”
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 (2006, neutral): “14 http://www.ecocyc.org (18). 15 http://www.ebi.ac.uk/genemark/ ( 19 ).”
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): “Four-gene-prediction programs were used to identify potential exon–intron structure: Fgenesh (Salamov and Solovyev 2000), GeneMark (Besemer and Borodovsky 2005), GlimmerHMM (Majoros et al.”
EGASP: the human ENCODE Genome Annotation Assessment Project (2006, neutral): “hmm program [60].”
Genome Majority Vote Improves Gene Predictions (2011, positive): “Therefore, our use of Prodigal gene maps instead of Glimmer3 [1], GeneMark [2], or older annotations appeared to be the most logical and conservative approach.”
Genetic Assessment of a Mini‐Core Subset Developed from the USDA Rice Genebank (2009, methodology): “Software applications for the heuristic algorithm include the FASTA program for sequence comparison (Altschul et al., 1990) and GeneMark for the ab initio gene search program ( Besemer and Borodovsky, 2005 ).”
BioJava: an open-source framework for bioinformatics in 2012 (2012, methodology): “The genome module is focused on the creation of gene sequence objects from the core module by supporting the parsing of GTF files generated by GeneMark (Besemer and Borodovsky, 2005), GFF2 files generated by GeneID (Blanco and Abril, 2009) and GFF3 files generated by Glimmer (Kelley et al ., 2011).”