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The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison.
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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.

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