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
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.
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.
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.
Hi! Check OrthoMCL. It is the best way to find orthologous genes.
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As I told you for those works you can use NCBI Blast, normally it shows different blast hits among various species.
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.
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.
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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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.
thanks guys for the suggestions
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.