EvidentialGene statistics

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Citations per year

Number of citations per year for the bioinformatics software tool EvidentialGene
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Tool usage distribution map

This map represents all the scientific publications referring to EvidentialGene per scientific context
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Protocols

EvidentialGene specifications

Information


Unique identifier OMICS_17501
Name EvidentialGene
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format GFF, XLS
Output format XLS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Donald Gilbert

Publication for EvidentialGene

EvidentialGene citations

 (25)
library_books

Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing

2018
Genome Biol Evol
PMCID: 5793845
PMID: 29385567
DOI: 10.1093/gbe/evy003

[…] bined tabular output from the searches was further run through two Perl scripts, “blast92gff3.pl” with additional options -lowscore 0.0001 -alignmax 9999 -exonType exon (http://arthropods.eugenes.org/EvidentialGene/evigene/scripts/blast92gff3.pl; last accessed January 14, 2018) and the “overbestgene2.pl” (http://iubio.bio.indiana.edu/gmod/tandy/perls/overbestgene2.perl; last accessed January 14, 2 […]

call_split

Differential gene expression in the evolution of sex pheromone communication in New Zealand’s endemic leafroller moths of the genera Ctenopseustis and Planotortrix

2018
BMC Genomics
PMCID: 5787247
PMID: 29373972
DOI: 10.1186/s12864-018-4451-1
call_split See protocol

[…] genome-guided assembly with Trinity. These two assemblies were combined using PASA []. Final optimized and cleansed transcriptome assemblies were obtained combining all SOAP and PASA assemblies with EvidentialGene, tr2aacds perl script []. The CDS sequences of the “okayset” of EvidentialGene were used for the subsequent analyses and from now on are referred to as genes. Assemblies are available i […]

library_books

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly

2018
GigaScience
PMCID: 5848817
PMID: 29342277
DOI: 10.1093/gigascience/gix137

[…] v0.10.2 [] based on HiSat2 [] alignment of RNA-sequencing reads to the newly generated A. ocellaris genome. The transcriptome assemblies were subsequently merged using the tr2aacds pipeline from the EvidentialGene [] package and similarly assessed for completeness using BUSCO, version 3 []. The final nonredundant transcriptome assembly, which was subsequently used to annotate the A. ocellaris gen […]

library_books

Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree

2017
GigaScience
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] removal, trimming, and coverage normalization, 55.2 million high-quality reads (38%) were used to assemble the transcriptome using de novo (Trinity and SOAP-Trans-denovo transcripts combined with the EvidentialGene pipeline) and genome-guided methods (PERTRAN). The PASA pipeline was used to integrate transcript alignments to the genome assembly from these sets of sequences, generating 54 320 Expre […]

library_books

Whole genome sequencing and SNV genotyping of ‘Nebbiolo’ (Vitis vinifera L.) clones

2017
Sci Rep
PMCID: 5725591
PMID: 29229917
DOI: 10.1038/s41598-017-17405-y

[…] of the library. The assembled transcript dataset was filtered of vectors using Seqclean (https://sourceforge.net/projects/seqclean/) and of redundant sequences and non-protein-coding assemblies using EvidentialGene ver. 2013.09.13 (http://arthropods.eugenes.org/EvidentialGene/). The filtered transcripts were incorporated into the PN40024 gene annotation using PASA ver. r2014-04-17. Assembled trans […]

library_books

Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species

2017
PLoS Negl Trop Dis
PMCID: 5685644
PMID: 29045404
DOI: 10.1371/journal.pntd.0005984

[…] Properly paired reads not filtered as S. mansoni were mapped to EvidentialGene-generated B. pfeifferi CDS with Bowtie2 []. Read abundance was quantified with RSEM (RNA-Seq by expectation maximization) []. Pairwise analyses for comparisons between control group and […]


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EvidentialGene institution(s)
Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK; Department of Biology, Indiana University, Bloomington, IN, USA; Cancer Center, Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA; Department of Organismic and Evolutionary Biology, and FAS Informatics Group, Harvard University, Cambridge, MA, USA; Department of Molecular Biology and Genetics, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, NY, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical School, Rochester, NY, USA; Department of Biology, University of Rochester, Rochester, NY, USA
EvidentialGene funding source(s)
This work was supported in part by the National Science Foundation (grant No. 0640462 to DGG), including genomics computational resources via TeraGrid amd XSEDE. Additional support was provided by a start-up grant by the University of Birmingham (UK) and earlier by the Center for Genomics and Bioinformatics (CGB) at Indiana University, which was supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. and US NIH R24 GM-084917.

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