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Protocols

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 citations

 (33)
library_books

A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

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 […]

library_books

Genome Sequences of Apibacter spp., Gut Symbionts of Asian Honey Bees

2018
Genome Biol Evol
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 […]

library_books

Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations

2018
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 […]

call_split

Comparative genomics reveals new single nucleotide polymorphisms that can assist in identification of adherent invasive Escherichia coli

2018
Sci Rep
PMCID: 5807354
PMID: 29426864
DOI: 10.1038/s41598-018-20843-x
call_split See protocol

[…] 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 […]

library_books

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

2018
BMC Genomics
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. […]

library_books

Transcriptome profiling with focus on potential key genes for wing development and evolution in Megaloprepus caerulatus, the damselfly species with the world's largest wings

2018
PLoS One
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., […]


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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]

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