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Exonerate specifications


Unique identifier OMICS_11232
Name Exonerate
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.2
Stability Stable
Maintained Yes




No version available



  • person_outline Guy St C Slater <>

Publication for Exonerate

Exonerate citations


Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] the blast 2.6.0+ software package [] with --evalue 1e-5 to search. reads were then separated into directories by gene and assembled with spades 3.10.1 []. the resulting contigs were processed with exonerate 2.2.0 [] with the protein2genome model using sequences from reference species with the best cumulative blast score to recover the exon sequences. we then merged the acquired exons of r. […]


Novel sequences, structural variations and gene presence variations of Asian cultivated rice

PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] to the novel sequences with ncbi-blastn. all rice proteins were downloaded from ncbi (12/15/2014) and were aligned to the novel sequences with ncbi-blastx. to get more informative alignments, exonerate was used to realign each sequence identified by blast around splice sites. evidencemodeler was used to combine and refine the ab initio predictions with rna and protein evidences. […]


Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] the protein sequences of the chicken (galgal4), turkey (umd2), duck (bgi_duck_1.0), and zebra finch (taegut3.2.4) were collected from ensembl. the protein sequence alignments were performed using exonerate (version 2.2.0) []. all rna-seq reads were aligned against the repeat-masked genome using tophat2 [], which generated evidence of splice sites, introns, and exons. additionally, trinity […]


Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] wgs project []) and transcoding regions was generated by pasa v2.1.0 [] and used to train all ab initio predictors except genemark es. alignment of est and protein evidence was performed with exonerate v2.2.0 [] using the coding2genome and protein2genome models respectively. maker was run using the trained gene predictors and performed est and protein alignments. following annotation […]


De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] for protein properties (family, domains and repeats, gene ontology term prediction and protein architecture) interproscan website was used (finn et al., ). in silico translation were performed with exonerate generic tool. exhaustive dynamic programming algorithm was employed to find the most likely hnt putative coding sequence in aedes aegypti genome (slater et al., ). reverse translation […]


Cross species inference of long non coding RNAs greatly expands the ruminant transcriptome

PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] on the sheep longlist for independent verification. the goat genome, by contrast, was annotated with a focus on protein-coding gene models [], by consolidating protein and cdna alignments—from exonerate [] and tblastn []—with the annotation tool evidence modeller (evm) []. consequently, there are no unambiguous lncrnas in the associated gtf […]

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Exonerate institution(s)
The Ensembl Group, EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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