Skip to content
The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison.
Perl R
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
0_Organisms_In_Ohnolog2.0
1_All_Genes
2_Paralogs
3_Orthologs
4_All_PC_Gene_Seqs
5_Run_synteny
6_CombineAllVertebrates
7_FilterOhnologs
8_GenerateOhnoFamilies
.gitignore
README.md

README.md

OHNOLOGS v2.0

OHNOLOGS v2.0 is a comprehensive repository for ohnologs retained from Whole Genome Duplications (WGDs) in the vertebrate genomes.

This repository contains all the codes and data used to construct OHNOLOGS v2.0 server.

More information can be found in the directories below:

  • 0_Organisms_In_Ohnolog2.0 Organisms and the outgroups included in OHNOLOGS v2.0.

  • 1_All_Genes Details on all the genes, Gene Ontology terms, chromosomal locations etc.

  • 2_Paralogs Details on candidate paralogs, their duplication timing, and consensus duplication timing from Ensembl.

  • 3_Orthologs Getting and preparing the orthologs from Ensembl among vertebrates and between vertebrates and outgroups for synteny analysis.

  • 4_All_PC_Gene_Seqs Including Amphioxus as an outgroup which is not covered by Ensembl.

  • 5_Run_synteny Run the synteny analysis to identify all ohnologs and their confidence score (q-score).

  • 6_CombineAllVertebrates Combining ohnologs from all vertebrates by taking a phylogenetically biased averaging of q-scores.

  • 7_FilterOhnologs Filter candidate ohnologs based on the three predefined (strict, intermediate and relaxed) q-score criteria.

  • 8_GenerateOhnoFamilies Generating ohnolog families for each criteria using ohnolog pairs.

If you use the data or code in the repository, please cite:

  • Singh P.P. and Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. bioRxiv.

  • Singh P.P., Arora J. and Isambert H. (2015) Identification of ohnolog genes originating from whole genome duplication in early vertebrates, based on synteny comparison across multiple genomes. PLOS Computational Biology.

You can’t perform that action at this time.