wjwei-handsome / ZeaGeneMap

A python tool for identifying the mapping of genes between two genomes.

GeneMap

GeneMap, A python tool for identifying the mapping of genes between two genomes by multi evidences.

Table of Contents

• Background
• Install
• Usage
• Badge
• Maintainers
• Contributing
• License

Background

When we have multiple genomes of the same species (or related species), we usually need to identify the gene mapping relationship between the two genomes(Gene A in genome a, mapped to gene B in genome B). We used four alternative evidence, including:

1. RBH Reciprocal Best BLAST Hits

   Despite these and other complication, the identification of reciprocal best hits for gene products is a good first approximation to the identification of orthologues in two or more organisms. It forms the basis for many orthology-finding tools, such as MCL, OrthoMCL and OrthoFinder. It can be carried out by carrying out BLAST+ searches using a short program, and this will be illustrated below.

2. ortholog OrthoFinder

3. synteny block McScanX

4. crosssmap minimap or AnchorWave

Install

TODO

$ pip3 install GeneMap

Usage

$ GeneMap.py -l list.txt -d work_dir -q GenomeA -t GenomeB -o output_prefix

Maintainers

@wjwei-handsome

Contributing

Feel free to dive in! Open an issue or submit PRs.

Standard Readme follows the Contributor Covenant Code of Conduct.

Contributors

Thanks @songtaogui for design ideas.

License

GPL-3.0 © Weiwenjie