Question: Finding orthologous gene within species
3
gravatar for Prasad
6.0 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

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

ADD COMMENTlink modified 4.2 years ago • written 6.0 years ago by Prasad1.6k

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.

ADD REPLYlink written 6.0 years ago by Whoknows840

thanks guys for the suggestions

ADD REPLYlink written 6.0 years ago by Prasad1.6k

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.

ADD REPLYlink written 4.3 years ago by Denise CS5.1k
2
gravatar for Prasad
6.0 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

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

ADD COMMENTlink written 6.0 years ago by Prasad1.6k
1

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.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by Bioinformatics_NewComer320
3
gravatar for Whoknows
6.0 years ago by
Whoknows840
Tehran,Iran
Whoknows840 wrote:

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.

ADD COMMENTlink modified 4.3 years ago • written 6.0 years ago by Whoknows840

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.

ADD REPLYlink written 6.0 years ago by qiyunzhu130
1
gravatar for konstantinkul
6.0 years ago by
Russian Federation
konstantinkul90 wrote:

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

ADD COMMENTlink written 6.0 years ago by konstantinkul90
0
gravatar for Whoknows
6.0 years ago by
Whoknows840
Tehran,Iran
Whoknows840 wrote:

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

ADD COMMENTlink written 6.0 years ago by Whoknows840
0
gravatar for Biogeek
4.3 years ago by
Biogeek400
Biogeek400 wrote:

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.

ADD COMMENTlink written 4.3 years ago by Biogeek400

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.

ADD REPLYlink written 4.3 years ago by Biogeek400
0
gravatar for Whoknows
4.3 years ago by
Whoknows840
Tehran,Iran
Whoknows840 wrote:

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.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Whoknows840

I'd be worried about the database date of that second link - WebmMGA - 2011, bit outdated?

ADD REPLYlink written 4.3 years ago by Biogeek400

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

ADD REPLYlink written 4.3 years ago by Whoknows840
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