Question: Cross Species Orthologues
0
gravatar for Apricimo
4.7 years ago by
Apricimo0
United States
Apricimo0 wrote:

Hello all,

 

I want to compare protein (amino acid) sequences of two organisms on a genome scale. That is, if I have organism A with 10 proteins (hypothetical) and another organism B with 10 proteins I would like to see what proteins in B are orthologues to A based on sequence identity/similarity. Theoretically where I can tabulate the results as follows. 

 

Protein from A        |         Protein from B and  Identity to A

1                             |               4               80%

2                             |               1                45%

3                             |               10              30%

4                            |                ---              No orthologue

5                            |                9                 65%

etc. 

I guess my question is what tools are out there to do this on a large scale not just one by one through NCBI blast.

 

Thank you

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Apricimo0
1
gravatar for h.mon
4.7 years ago by
h.mon29k
Brazil
h.mon29k wrote:

A simple (and naive) way of doing this is performing BLAST searches of one proteome against the other and picking reciprocal best hits, filtering in some way - percent identity or e-score.

There are several programs which perform ortholog searches, OrthoMCL and OMA being two widely used choices.

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by h.mon29k
0
gravatar for dago
4.7 years ago by
dago2.6k
Germany
dago2.6k wrote:

Look into Biostars, there are many similar posts:

Ortholog Protein Finding Tool

ADD COMMENTlink written 4.7 years ago by dago2.6k
0
gravatar for Apricimo
4.7 years ago by
Apricimo0
United States
Apricimo0 wrote:

This is exactly the kind of thing I needed.

 

http://omabrowser.org/oma/genomePW/

 

Preferred ID is to use protein names used by kegg "Source ID"

ADD COMMENTlink written 4.7 years ago by Apricimo0
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