Question: Ortholog Detection Tool
4
gravatar for Gorysko
8.8 years ago by
Gorysko100
Germany
Gorysko100 wrote:

Dear all nowadays I want to detect orthologs in wide group of bacteria, and I've choose blast method BRH. I've found quite good topics here about it http://biostar.stackexchange.com/questions/5104/how-to-prove-an-ortholog-does-not-exist-in-a-given-genome

http://biostar.stackexchange.com/questions/7591/what-is-the-best-method-to-find-orthologous-genes-of-a-species

http://biostar.stackexchange.com/questions/6161/blast-reblast-to-verify-homologies

http://biostar.stackexchange.com/questions/6161/blast-reblast-to-verify-homologies

But a lot of tools described there aren't exist or don't work correctly on my workstation (debian testing 16+8 gb RAM)

So could I ask you about software tool of detection orthologs or way to write a script in bash or in python Thank You for attention

orthologues • 4.5k views
ADD COMMENTlink modified 8.7 years ago by Asaf8.4k • written 8.8 years ago by Gorysko100
6

I don't think bash/python will help you in this case. It sounds like you need to work on your system administration skills. What tools have you tried to install on your system and what do you mean by "don't work correctly"? Error messages are helpful.

ADD REPLYlink written 8.8 years ago by Neilfws49k
1

OrthoMCL and Inparanoid Inparanoid gives only empty files OrthoMCL has problems with MySQL

ADD REPLYlink written 8.8 years ago by Gorysko100
2
gravatar for ALchEmiXt
8.8 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

You might want to check the basic approaches of "reciprocal FASTA" where usually hits are identified as amino acid identity >40% over at least 80% of the total length of the protein....

For the mapping you can basically use whatever mapper you find useful. Usually FASTA, MUMmer, or BLAST are used.... You missed this biostar thread about it.

A simple google gave me the reciprocal fasta script at Sanger.

A starter at least.

ADD COMMENTlink modified 14 months ago by RamRS30k • written 8.8 years ago by ALchEmiXt1.9k

reciprocal fasta script at Sanger this fasta script is too old it's need PSU module which is not fully available. But the idea of reciprocal fasta is good -I could make two protein blasts with key "-m 8" and "-b 1" and I'll have two tables which i should only compare

ADD REPLYlink written 8.8 years ago by Gorysko100
2
gravatar for Asaf
8.8 years ago by
Asaf8.4k
Israel
Asaf8.4k wrote:

Instead of predicting them you can refer to the already predicted groups of ortholog proteins in the NCBI Protein Clusters database: http://www.ncbi.nlm.nih.gov/proteinclusters . I use this database to find orthologs of bacterial genes and it works quite good.

ADD COMMENTlink written 8.8 years ago by Asaf8.4k
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