ExonHunter statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Protein-coding gene prediction chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

ExonHunter specifications


Unique identifier OMICS_07785
Name ExonHunter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


Add your version


  • person_outline Broňa Brejová <>

Publications for ExonHunter

ExonHunter in publications

PMCID: 5908196
PMID: 29630596
DOI: 10.1371/journal.pgen.1007322

[…] (illumina, america), and amplified using truseq pe cluster kit (illumina, america), and then sequenced in solexa sequencing machine (illumina, america). gene calls were generated using fgenesh [], exonhunter [] and augustus version 2.7 []., annotation of the genes encoding carbohydrate active enzymes involved in plant cell wall degradation (pcwdcazome) in the nine trichoderma genomes […]

PMCID: 5578839
PMID: 28860241
DOI: 10.1128/genomeA.00851-17

[…] the sequence complementary to this motif was also found in the template domain of putative telomerase rna (ter1)., to annotate the nuclear genome, protein-coding genes were predicted using exonhunter () (with custom parameter training) and augustus () (with model for debaryomyces hansenii). exonhunter reported 5,827 protein-coding genes, and augustus 5,502. according to trnascan-se […]

PMCID: 3964345
PMID: 23485966
DOI: 10.1038/nature12031

[…] julian gough at superfamily, and christophe dessimoz for oma; c. seed and f. jarero for laboratory assistance; john overington and bissan al-lazikani; dr. brona brejová for predicting genes with exonhunter. p.d.o. and n.p.s. were supported in part by a bbsrc grant (bbg0038151) to p.d.o. p.d.o., m.z. was supported by a syntax joint-uk research council grant. the european research council […]

PMCID: 3484023
PMID: 22876864
DOI: 10.1186/1471-2164-13-382

[…] with identity cut-off of 90%., the gene prediction of m. brunnea was performed independently with a combination of three gene prediction program, including genemark (v2.3), augustus (v2.3.1), and exonhunter. the gene models were selected and manually curated by argo genome browser (v 1.0.31, http://www.broadinstitute.org/annotation/argo/). the gene models were aligned using blastp […]

PMCID: 2785426
PMID: 19997615
DOI: 10.1371/journal.pone.0008206

[…] small nucleolar rnas (snornas) deposited in the rfam database (ftp://selab.janelia.org/pub/rfam/) and ncbi genbank (http://www.ncbi.nlm.nih.gov/genbank). we also masked the repeat sequences using exonhunter (http://lifecenter.sgst.cn/schistosoma/en/schistosomacnindexpage.do) and repeatmasker programs (http://www.repeatmasker.org), and ones mapped to protein-coding exons. the data indicated […]

To access a full list of publications, you will need to upgrade to our premium service.

ExonHunter institution(s)
Department of Computer Science, Faculty of Mathematics, Physics, and Informatics, Comenius University, Bratislava, Slovakia

ExonHunter reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ExonHunter