search

apetkau / orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
80 stars 36 forks source link

Multiple species #45

Open ardy20 opened 3 years ago

ardy20 commented 3 years ago

Hello

Could you please help me to run your pipeline? I only have one gene that I would like to find its orthologs in 136 sequenced plant genomes.

Do I need to download the sequenced genomes (in a folder) or this tool works with databases?

Does this tool create and set up MySql?

Please give me an example script as well.

Regards

apetkau commented 3 years ago

@ardy20 you may want to consider looking at other ortholog-detection software (https://omabrowser.org/standalone/) or pangenome analysis software (such as Roary https://sanger-pathogens.github.io/Roary/) since they are more up-to-date. This project is no longer being developed and I do not know how easy or difficult it is to get this installed right now.

Also note that OrthoMCL (along with many other ortholog detection software) analyzes all genes in all genomes, not just a single gene. You could likely do most of what you want by directly running BLAST of your gene against a database of all genes in all 136 genomes, though to separate out orthologs from paralogs etc would require a bit of additional work (maybe the BLAST matches from this stage could be input to OrthoMCL or other software to reduce the amount of data you work with and help separate out orthologs from paralogs).

However, if you'd like to get this working please refer to the Installation guide along with a walkthrough of a small data analysis on a set of genome https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/orthomcl.

Do I need to download the sequenced genomes (in a folder) or this tool works with databases?

You need to have all genomes downloaded and split into individual genes (as amino acids). The genes must all be in a single fasta file, one per genome.

Does this tool create and set up MySql?

Some of the provided setup scripts will build a database but you need to install mysql and setup appropriate users yourself.

Please give me an example script as well.

This is an example walkthrough of OrthoMCL https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/orthomcl.

apetkau commented 3 years ago

I will also refer you to the main OrthoMCL website https://orthomcl.org/orthomcl/app/