Question: Protein Protein Interaction Prediction For Orthologue Proteins
2
gravatar for Sudeep
8.6 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

Hi all, What are the existing methods (stand alone tools) available for protein protein interaction prediction for orthologue proteins ? I know that STRING has some interaction data from homology modeling and I am working on a species with very little interaction data, so I did not have much success with any other databases. For ppi prediction from orthologs I came across this perl module and InteroPorc stand alone tool. But does someone has any other suggestions or experience with such stand alone tools for ppi prediction for orthologs ?

Thank you

ppi • 2.5k views
ADD COMMENTlink written 8.6 years ago by Sudeep1.6k
2
gravatar for Paul Denny
8.5 years ago by
Paul Denny30
Paul Denny30 wrote:

Try Perl module described in this paper: "Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161927/?tool=pubmed It accepts as input a list of Ensembl gene accession numbers from any of the vertebrate or metazoan genomes in Ensembl, which includes Bos taurus.

ADD COMMENTlink written 8.5 years ago by Paul Denny30
1
gravatar for Khader Shameer
8.6 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Homologous pairs of protein interactions across different organisms are called as interologs.

Information about interologs will enable annotation transfer between genomes and may also help to derive evolutionarily conserved interaction modules.

Please check following databases:

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by Khader Shameer18k

Thank you (for the articles and databases). Interolog/Regulog Database is only dealing with "model organisms", so I am leaving that out completely.

ADD REPLYlink written 8.6 years ago by Sudeep1.6k

What is your organism ?

ADD REPLYlink written 8.6 years ago by Khader Shameer18k

its actually cattle

ADD REPLYlink written 8.5 years ago by Sudeep1.6k

That's a vague description for an "organism" name in the context of biological. Can you please give the species/sub-species name ?

ADD REPLYlink written 8.5 years ago by Khader Shameer18k

to define it clearly it is Bos taurus (or commonly cattle)

ADD REPLYlink written 8.5 years ago by Sudeep1.6k
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