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Eval specifications

Information


Unique identifier OMICS_14471
Name Eval
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data gene annotations
Input format GTF
Operating system Unix/Linux, Windows
Programming languages Perl
License BSD 2-clause “Simplified” License
Computer skills Medium
Version 2.2.8
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michael Brent <>

Publication for Eval

Eval in pipelines

 (2)
2018
PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] transcript sequences in fasta format were created using the gene model information from braker1 using gff2fasta (http//github.com/minillinim/gff2fasta) tool. gene model structure was evaluated using eval () and genome completeness was evaluated with busco (). gene ontology (terms) assigned to predicted transcripts and go plots were produced using wego (http://wego.genomics.org.cn)., comparative […]

2007
PMCID: 1783852
PMID: 17229318
DOI: 10.1186/1471-2164-8-18

[…] script was used to generate gene transfer format (gtf) files corresponding to the predicted and experimentally validated gene models from blat alignments of the cds to the arabidopsis genome. the eval software package [] was then used to make comparisons between our experimentally verified intergenic genes and the underlying twinscan and eugene predictions. sensitivity and specificity […]


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Eval in publications

 (6)
PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] transcript sequences in fasta format were created using the gene model information from braker1 using gff2fasta (http//github.com/minillinim/gff2fasta) tool. gene model structure was evaluated using eval () and genome completeness was evaluated with busco (). gene ontology (terms) assigned to predicted transcripts and go plots were produced using wego (http://wego.genomics.org.cn)., comparative […]

PMCID: 5674158
PMID: 28994416
DOI: 10.1038/cr.2017.124

[…] was assessed by comparing the predicted protein sequences to the pfam 31.0 database and to busco v2. then, the sensitivity and specificity of the gene, exon and nucleotide level were evaluated using eval v2.2.8 by using mrna sequences retrieved from the ncbi nucleotide database or high-expression genes assembled from mrna-seq data. a detailed description can be found in ., orthofinder was used […]

PMCID: 4414376
PMID: 25908251
DOI: 10.1186/s13059-015-0623-3

[…] two n-scan gene prediction sets, one based on amel_4.5 and the other based on bimp_2.0 as the informant genomes. the amel_4.5 as the informant set was chosen as the best prediction set based on eval analysis [] against the refseq and gnomon annotations for b. terrestris. insufficient b. impatiens transcriptome data were available to generate bimp_2.0-amel_4.5 and bimp_2.0-bter_1.0 specific […]

PMCID: 4214606
PMID: 25319552
DOI: 10.1186/1745-6150-9-20

[…] 3′ utr., 6. we used several approaches to identify and correct errors in the gtf file that serves as our annotation of the new rhesus genome (macam_annotation_7.6, additional file ). these included eval [] and gffread from the cufflinks2 software packages []. we used custom scripts to ensure that every cds range had a corresponding exon range and to remove duplicate transcripts. to correct […]

PMCID: 2996948
PMID: 20609256
DOI: 10.1186/1471-2164-11-420

[…] with augustus trained for zea mays. both sets of maker-produced gene models were saved in gff3 [] format and simple intron/exon structure statistics were calculated against them using the program eval [,] the maker runs were viewed and evaluated using the apollo genome annotation curation tool []. the peptide sequences corresponding to both sets of maker gene predictions were searched […]


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Eval institution(s)
Department of Computer Science and Engineering, Washington University, Saint Louis, MO, USA
Eval funding source(s)
This work was supported by grant DBI-0091270 from the National Science foundation and grant HG02278 from the National Institutes of Health.

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