Exonerate protocols

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Exonerate specifications

Information


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

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  • person_outline Guy St C Slater <>

Publication for Exonerate

Exonerate in pipelines

 (46)
2018
PMCID: 5801409
PMID: 29456553
DOI: 10.3389/fgene.2018.00019

[…] on the genome assembly (rproc1 version) and gene predictions (vectorbase 1.3 version) performed by and deposited in vectorbase database. uncompleted or fragmented genes were re-predicted using exonerate software version 2.2 () based on insect orthologous proteins sequences deposited in ncbi databases. the re-prediction results were manually curated and edited when needed. re-predicted […]

2018
PMCID: 5844311
PMID: 29326229
DOI: 10.1534/g3.117.300421

[…] newly sequenced strains, 11,382 proteins of the type strain r. mackenziei cbs 650.93 (jybu00000000) were aligned to the genome of the strains ihm 22877 and dh24460 using the homology-based predictor exonerate v. 2.2.0 () with the parameters–model protein2genome–percentage 90. pathway and kog prediction were assessed using kaas (bidirectional best hit) (). putative secreted proteins […]

2018
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] v 4.33 (--es --fungus --cores 16) [] and codon quarry v1.2 [] assisted by rna-seq alignments. in order to capture highly polymorphic genes, ptr bfp reference proteins [] were aligned using exonerate v2.2.0 (--showvulgar no --showalignment no --minintron 10 --maxintron 3000) mode protein2genome []. the final gene prediction sets were predicted via evidencemodeller v1.1.1 [] using […]

2018
PMCID: 5915941
PMID: 29697817
DOI: 10.1093/gbe/evy066

[…] of orthologous sequences using mafft l-insi () and generated phmms from each alignment using hmmer 3.1b1 (www.hmmer.org). we translated transcript sequences into all six possible reading frames with exonerate, version 2.2.0 () and searched with each phmm the translated transcriptome and genome (predicted proteins) data using hmmsearch with default options (hmmer 3.1b1)., because dnmt1, dnmt3, […]

2018
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 in publications

 (222)
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. […]

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. […]

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 […]

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 […]

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 […]


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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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