How can I specify my proteins gene to orthoMCL
I'm using orthoMCL, all work fine. But i dont know how to specify to orthoMCL which proteins belong to which genes and to which species. I have searched over Internet i have not seen anything Tank you.
• 2,598 views
•
link
updated
by
natasha.sernova
•
written
by
Esaie
•
written
by
Esaie
1 answer
See this paper: Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196566/
“How the tool processes your proteins: This protocol maps your proteins to groups in OrthoMCL-DB. To understand how OrthoMCL-DB is created, please see the OrthoMCL- DB Methods page.”
OrthoMCL Algorithm:
https://docs.google.com/document/d/1RB-SqCjBmcpNq-YbOYdFxotHGuU7RK_wqxqDAMjyP_w/pub
• 1 views
•
link
written
by
natasha.sernova
Log in to answer this question.
More posts like this
-
FlowJo Parameter Meaning
written by mialopez97 •
-
How to make blast go on to the next protein
written by marcelofolhas •
-
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
written by Esaie
-
How can I run All-v-all BLAST
written by Esaie
-
phylogenetic tree after ortholog finding by orthoMCL
written by Mehmet
-
Where can I find the Interpro/OrthoMCL annotation of all the proteins of a species?
written by cyril-cros
-
finding orthologs in four genomes
written by Mehmet
-
categorising proteins into families when you have amino acid sequences
written by mwanerhi erfgtr •
-
Orthologous non-coding genes
written by int11ap1
-
How To Correctly Classify Gene Families?
written by GR
Did you find the answer to this? I am also search for how to format the gene --> mapping and feed it into the program.