Plant orthologous genes
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3.8 years ago
pixie@bioinfo ★ 1.5k

Hello, I have a list of gene IDs from rice. I want to have the orthologous genes in Arabidopsis, maize , wheat etc.

Can someone suggest a database from which I can bulk download ? I wish to have the ortholog information for all genes in rice. Any suggestion is greatly appreciated

gene • 1.8k views
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A past thread of interest: A: Plant orthologous gene database

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@genomax, It looks like the last update to this database was in 2015. Finding orthologs manually is a much better option as many of the genomes of interest here have gone through multiple assembly and annotation iterations and several have complete genomes from multiple cultivars. For example, a full chromosome wheat assembly was published last week.

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You can have the orthologous genes in Arabidopsis for all rice genes at Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html#)

The best way is to do the reciprocal BLAST analysis of the transcript sequences and retain the best hits from two species to identify the orthologous genes.

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JC 13k

You can use the Compara database from Ensembl Plants using their API or BioMart.

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3.8 years ago

PLAZA should be your go to resource for this kind of questions

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geneticatt ▴ 140

The way that I've handled this issue in the past is by downloading the amino acid sequences for each species of interest from their respective databases and using OrthoFinder's phylogenetic orthology inference tool. The sequences will cluster into groups of orthologs and paralogs.

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