How can I identify all homologues between two fully assembled genomes?

Question

[ChrisM]

I'm trying to identify the homologues of all genes between two fully assembled bacterial genomes (e.g. Bacillus subtilis and Staphylococcus aureus) in batch. It looks like relevant data are available on the NCBI COG database, but their 2012 COG software won't compile so I haven't been able to attempt this particular method. As an alternative to using this software, is there a flat file of gene name to COG (or equivalent) that I could just download then match in Excel? I greatly appreciate all suggestions. Thank you in advance!

Regarding the Cog Software: I downloaded the source code from ftp://ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/ and I'm using Ubuntu 16.04 xenial.

Error:

g++ -O2 -c main.cpp

In file included from main.cpp:2:0:

os.h: In function ‘void myOpenDir(const char*)’:

os.h:13:16: error: ‘chdir’ was not declared in this scope

chdir(dirpath); ^

Makefile:9: recipe for target 'main.o' failed

make: * [main.o] Error 1

[GenoMax]

You may be able to use MBGD to get this information.

[ChrisM]

Thank you! Also, after much searching, I also found: https://omabrowser.org/oma/genomePW/ which has been fantastic.

Answer 1

[h.mon]

Add #include <unistd.h> to os.h, this should fix COGsoft compilation issue.

[serg]

I had the same problem, this solution worked for me. Thanks