Comparative Genome Search

Among bamboo relative plants, you may use this search function to find orthologous genes (determined by OrthoMCL algorithm) that are include one set of genomes and exclude another set.


Find genes that have orthologs : Including  Excluding

Panicum virgatum
Setaria italica
Sorghum bicolor
Zea mays
Oryza sativa
Phyllostachys edulis
Brachypodium distachyon
Arabidopsis thaliana
Note: Phylogenetic tree was produced based on ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene

Gene: (Optional) e.g. PH01000000G0240 or PH01000000G0240;PH01000053G0650

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and Keywords: (Optional)
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Orthologs are homologs seperated by speciation events. Detection of orthologs is becoming much more important with the rapid progress in genome sequencing.

You may use this search function to perform comparative analyses of orthologous genes using OrthoMCL, which is a genome-scale algorithm for grouping orthologous protein sequences:

Function 1. Find orthologs present in one set of genomes and number variation in each present ortholog group (e.g. one or more species selected from left box)

Example:

You would like to find all orthologous genes that are present in BOTH bamboo and Oryza sativa.

Steps:

a) Select Oryza sativa from the left box

b) Click on submit.

Function 2. Find orthologs present in one set of genomes (e.g.one or more strains selected from left box) while absent from another set (e.g. one or more genomes selected from right box).

Example:

You would like to find all orthologous genes that are present in BOTH bamboo and Oryza sativa but NOT present in Zea mays.

Steps:

a) Select Oryza sativa from the left box

b) Select Zea mays from the right box

c) Click on submit.

Function 3. Find a list of genes in bamboo species that do not have orthologs in another species.

Example:

You would like to find all genes in bamboo

Steps:

a) NOT Select anything from the left box and the right box

b) Click on submit.

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