OrthoVenn protocols

View OrthoVenn computational protocol

OrthoVenn statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Gene orthology prediction Venn diagram creation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

OrthoVenn specifications

Information


Unique identifier OMICS_08536
Name OrthoVenn
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yong Q. Gu <>

Publication for OrthoVenn

OrthoVenn in pipelines

 (9)
2018
PMCID: 5807354
PMID: 29426864
DOI: 10.1038/s41598-018-20843-x

[…] was used to study crispr. to find gene content differences, blastp comparison (e-value cutoff 1e-5) and markov clustering (inflation factor 2.0) were performed by orthovenn using protein sequences. a correction with local blastn was performed to recruit genes located at the beginning or end of contigs., the harvest suite for rapid-core genome alignment […]

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

[…] with busco (). gene ontology (terms) assigned to predicted transcripts and go plots were produced using wego (http://wego.genomics.org.cn)., comparative genomic analysis was performed using orthovenn () with default cut-off values, which uses a modified version of the orthomcl () algorithm for identification of orthologous gene clusters based on sequence homology. m. domestica proteins […]

2018
PMCID: 5954486
PMID: 29611344
DOI: 10.1111/1751-7915.13259

[…] from genbank (sillo et al., ). blast analysis was performed to compare h. occidentale sequences with h. irregulare and h. annosum genome sequences or h. irregulare proteome (13 275 proteins). orthovenn server (wang et al., ) was used to determine orthologous gene families., secretome was identified by scanning complete orfs using phobius (käll et al., ), which generated a list […]

2017
PMCID: 5486027
PMID: 28587273
DOI: 10.3390/ijms18061204

[…] []. the predicted proteome of d. pteronyssinus is a combination of proteins derived from the transcriptome and two ab initio gene prediction to be described []. for the orthology analysis with orthovenn, amino acid sequences of the predicted proteases from each of the three mites outlined in were input as separate fasta files () and the default threshold values were used (e-value 10−5 […]

2017
PMCID: 5509663
PMID: 28706242
DOI: 10.1038/s41598-017-05478-8

[…] phylip file containing the input genomic sequences., the complete proteome of the three fungal species i.e. a. rolfsii, g. luxuricans, c. subvermispora, m. roreri were downloaded from ncbi database. orthovenn server was used for identification of shared and unique orthologous gene families clusters in the above mentioned fungal genomes., the whole-genome sequence and annotation of athelia […]

OrthoVenn in publications

 (31)
PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] with busco (). gene ontology (terms) assigned to predicted transcripts and go plots were produced using wego (http://wego.genomics.org.cn)., comparative genomic analysis was performed using orthovenn () with default cut-off values, which uses a modified version of the orthomcl () algorithm for identification of orthologous gene clusters based on sequence homology. m. domestica proteins […]

PMCID: 5913662
PMID: 29635372
DOI: 10.1093/gbe/evy076

[…] and annotation for all four apibacter genomes was done on the rapid annotation using subsystem technology (rast) 2.0 platform (). orthologous gene clusters were identified and compared using orthovenn (). single-copy orthologs (1,132 proteins; 401,782 positions) were retrieved using orthofinder (), aligned with muscle (), and concatenated to build a phylogenetic tree using the lg amino […]

PMCID: 5954486
PMID: 29611344
DOI: 10.1111/1751-7915.13259

[…] de novo assembled from rna‐seq reads were relatively complete, and species‐unique genes may only account for about 10% of total genes., consistently with the above findings, comparative analysis by orthovenn predicted 7999 orthologous groups (ogs) shared by both h. occidentale and h. irregulare, as well as 233, 371 and 259 ogs unique for the h. occidentale isolates hoc‐pfc5313, hoc‐pfc5396 […]

PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] protein sequences were filtered using ≥ minimum length of 10 amino acids. then the orthomcl steps were performed as described in orthomcl manual []. the results from orthomcl [] were visualized by orthovenn []., all four assemblies were aligned with v. vinifera (pn40024 12x.v2, vcost.v3) reference genome [] by mummer [] and then the same steps were performed as noted for the bac alignment. […]

PMCID: 5766104
PMID: 29329292
DOI: 10.1371/journal.pone.0189898

[…] request., overlaps were determined via comparative sequence similarity applying a reciprocal blast search using an in-house perl script that reverts to blastp with a significant e-value of 1e-7. orthovenn [] was further applied to categorize the transcripts into orthologous clusters. it simultaneously annotates the clusters, which were extracted to compare among the three transcriptomes., […]

OrthoVenn institution(s)
USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, USA
OrthoVenn funding source(s)
U.S. National Science Foundation [IOS 0822100]; United State Department of Agriculture, Agriculture Research Service CRIS project [5325-21000-021]

OrthoVenn reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review OrthoVenn