Best Method to Find Homologous Genes of a Species?
So, you have a gene of of interest that you would like to compare between homologues. SInce number of genome sequences are increasing day by day so it is the most obvious question that what is the best method to find homologous genes across different organisms? So before starting, let's clear some terms. Homologous gene is a broad term which can be used synonymously with other terms also. Some of them are :
Homologous : shared ancestry of a gene in two different species. For instance, hemoglobins genes of human and rat.
Paralogous : shared ancestry caused by gene duplication e.g. hemoglobin A, hemoglobin A2, hemoglobin B and hemoglobin F genes in human genome
Ohnologous : paralogs originated by a process of whole-genome duplication.
Xenologous : homologs resulting from horizontal gene transfer between two organisms
I have already stated so many times that NCBI is my first love. So whenever I look for homologs; first of all I use NCBI BLAST services. BLAST can give you a good rough idea about different homologs of your gene of interest. A very good tutorial to find out homologous gene in other organism is provided by NCBI itself that can be found HERE. To find a homolog for a gene in another organism, you can search NCBI with gene name, accession number and sequences.
In other way, you can identify the homologs of your gene interest from the pre-computed databases. Huge numbers of databases are there to help you out. The best thing about using an existing database is that more sophisticated methods for detecting orthologs than simple BLAST searches have been used to prepare the database and since everything is already pre-computed, so it s much faster. So roughly there databases are prepared on two different but quite dependent principle :
- Phylogeny-based analysis
- Blast-based analysis
First of all, let me clear it that i am not a Bioinformatician. i am simple plant biology researcher who face problem in her daily research life and who bother to post solution of those problem on this webpage. That's it.