OrthoVenn pipeline

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

 (3)
2018
PMCID: 5954486
PMID: 29611344
DOI: 10.1111/1751-7915.13259

[…] from genbank (sillo et al., 2015). 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., 2015) was used to determine orthologous gene families., secretome was identified by scanning complete orfs using phobius (käll et al., 2007), which generated a list […]

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

[…] [42]. the predicted proteome of d. pteronyssinus is a combination of proteins derived from the transcriptome and two ab initio gene prediction to be described [26]. for the orthology analysis with orthovenn, amino acid sequences of the predicted proteases from each of the three mites outlined in table 1 were input as separate fasta files (supplemental) and the default threshold values […]

2017
PMCID: 5778601
PMID: 29293976
DOI: 10.1093/gbe/evx279

[…] analyses. the final databases of candidate toxins for each species were manually curated and orthologous clusters of putative toxins shared by the three species were identified and annotated with orthovenn (wang et al. 2015)., phylogenetic analyses of individual toxin families including amphinomid homologs were performed to validate the orthology predictions derived from the venomics pipeline […]

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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