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GeneMarkS-T specifications

Information


Unique identifier OMICS_08422
Name GeneMarkS-T
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mark Borodovsky

Publication for GeneMarkS-T

GeneMarkS-T citations

 (3)
library_books

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

2017
F1000Res
PMCID: 5553090
PMID: 28868132
DOI: 10.5256/f1000research.11392.r19894

[…] was used, following its instructions. we required a minimum frequency of each alternative event >10%., for the prediction of protein coding capability of novel isoforms, genemarks-t (version 5.1; http://exon.gatech.edu/genemark/) with default parameters was used. for gene enrichment analysis, david (version 6.8) was used., the mappable length is a good […]

library_books

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non model) Organisms

2017
PMCID: 5607918
PMID: 28518075
DOI: 10.3791/55009

[…] the "data output" section, type a unique name for the de novo assembly. this will create a folder of rnaquast output files inside of the folder "b_rnaquast_output." select additional options in the "genemarks-t gene prediction," "busco," and "parameters" sections. select prokaryote in the "genemarks-t gene prediction" section if the organism is not eukaryotic.run busco to select the browse […]

library_books

A novel codon based de Bruijn graph algorithm for gene construction from unassembled transcriptomes

2016
Genome Biol
PMCID: 5114782
PMID: 27855707
DOI: 10.1186/s13059-016-1094-x

[…] were compared with the four other gene prediction pipelines using a publicly available rna-seq dataset (srr1045067). because the running time and memory usage of estscan, transdecoder, prodigal, and genemarks-t were negligible, these tools were not included in this comparison. we ran all four programs on a node with 2.13 ghz intel xeon processors using eight cpus on the linux (red hat 6.3) […]


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GeneMarkS-T institution(s)
Georgia Institute of Technology, Atlanta, GA, USA
GeneMarkS-T funding source(s)
National Institutes of Health (NIH) [HG000783 to M.B.]

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