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ExonHunter specifications

Information


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

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Maintainer


  • person_outline Broňa Brejová <>

Publications for ExonHunter

ExonHunter in publications

 (8)
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 […]


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

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