Finding orthologous gene within species
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6.8 years ago
Prasad ★ 1.6k

Dear all,

I have checked many post in biostar and other blogs to find orthologous and paralogous gene identification across/within the species. Most of them are suggesting for Best Reciprocal Blast Method(BBRM). But i have 2 leaf and 2 rhizome transcript samples. I have to find out orthologous and paralogous genes between these set. Shall i use BRBM method or are there any other better way to do it.

Please suggest any tools.

Thanks all

orthologous paralogous homologous • 3.2k views
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Hi, You just download NCBI blast toolkit then make blast database via makeblastdb and finally search your sequences within target set by blastn (DNA) or blastp (for protein) ,

but i think NCBI/Blast can handle your job as well.

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thanks guys for the suggestions

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There are resources with orthologues and paralogues already calculated that may be useful to you, e.g. orthologues to the A. thaliana PAD4 gene. Ensembl Plants has 44 species.

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6.8 years ago
Prasad ★ 1.6k

Thanks for the suggestion.

If i am not mistaken, you are suggesting BRBM (Best Reciprocal Blast method) to use. If so i will find orthologous genes between samples. Could you please suggest any way to find paralogous genes as well

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For paralogous, you will blast your sequences against themselves. The first hit other then - gene itself and its isoform [if present] would be the best hit. That will be its paralogous hit.

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6.8 years ago
Whoknows ▴ 880

Hi, You just download NCBI blast toolkit then make blast database via makeblastdb and finally search your sequences within target set by blastn (DNA) or blastp (for protein) ,

but i think NCBI/Blast can handle your job as well.

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Agree with this comment, and my two cents are that: The problem Prasad faces is that two leaf and two rhizome are not treated as different organisms in the default NCBI database, in which case, he has to re-define taxonomy. The straightforward way one can think about is to make BLAST databases by their own. Simply prepare four "genome" files and make them a BLAST database will do the job.

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6.8 years ago
konstantinkul ▴ 100

Hi! Check OrthoMCL. It is the best way to find orthologous genes.

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6.8 years ago
Whoknows ▴ 880

As i told you  for those works you can use NCBi Blast page , normally it shows different blast hits among various species.

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5.1 years ago
Biogeek ▴ 400

OrthoMCL / evidential gene.

Also conditional reciprocal best blast / RBH are good methods for determining pretty confident orthologues. Paralogues may be harder to detect I guess.

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Mind you I think RBH/CRBB is the easiest way forward.

https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh -Use this python script.

It needs NCBI+ to be installed. Set NCBI+ in your job PATHs, voila.

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5.1 years ago
Whoknows ▴ 880

Hi

what we do in plant studies is using COG/KOG analysis or cluster of orthologous groups of proteins.

You can upload your protein sequences into WebMGA and it gives you ~25 cluster of protein groups across different species.

Hope it helps you.

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I'd be worried about the database date of that second link - WebmMGA - 2011, bit outdated?

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Yes you are right but WebMGA is easy to use, but for more updated version you could use EggNOG database, which is recently updated.

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