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Ortholog-Finder specifications

Information


Unique identifier OMICS_23371
Name Ortholog-Finder
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A GenBank file or an amino acid sequences file.
Input format GenBank,FASTA
Output data A multi-FASTA format, which includes sequence data of each ortholog or a multi-FASTA-like format that includes all ortholog sequence data in one file.
Output format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 4.07
Stability Stable
Requirements
BLAST+, FastTree, MAFFT, Gblocks, Bioperl, EMBOSS, mcl, OrthoMCL, Java Runtime Environment
Maintained Yes

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Maintainer


  • person_outline Tokumasa Horiike <>

Publication for Ortholog-Finder

Ortholog-Finder in publications

 (2)
PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] evidence and three ab initio gene prediction approaches. we set maker2 to annotate the 2,210 scaffolds longer than 5,000 bp. for protein homology evidence, we used an ortholog database created with ortholog-finder http://www.grl.shizuoka.ac.jp/~thoriike/ortholog-finder and the protein databases of the species described in table . ab initio gene prediction was accomplished by (1) training snap […]

PMCID: 5313534
PMID: 28261177
DOI: 10.3389/fmicb.2017.00218

[…] (at least two are required) is selected as the best synteny ortholog. the whole workflow is depicted in figure ., the script is available for download at https://github.com/danielwuethrich87/synteny_ortholog_finder.git., between the genome of fam21731 and the other 17 l. parabucheri strains and the l. buchneri stains (cd034, nrrl b-30929) the synteny orthologs were identified using the synorf […]


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Ortholog-Finder institution(s)
Department of Biological and Environmental Science, Shizuoka University, Japan; The Genome Institute, Japanese Foundation of Cancer Research, Tokyo, Japan; Department of Economics, Chiba University of Commerce, Ichikawa, Japan; Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, Kanagawa, Japan; School of New Sciences, Daegu Gyoungbook Institute of Science and Technology, Daegu, Korea
Ortholog-Finder funding source(s)
Supported by the Japan Society for the Promotion of Science, Grant Number 22710184.

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