Question: How can I identify all homologues between two fully assembled genomes?
1
gravatar for ChrisM
2.6 years ago by
ChrisM10
Seattle
ChrisM10 wrote:

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

cogs bacteria • 750 views
ADD COMMENTlink modified 2.6 years ago by genomax90k • written 2.6 years ago by ChrisM10

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

ADD REPLYlink written 2.6 years ago by genomax90k

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

ADD REPLYlink written 2.6 years ago by ChrisM10
1
gravatar for h.mon
2.6 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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

ADD COMMENTlink written 2.6 years ago by h.mon31k

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

ADD REPLYlink written 2.3 years ago by serg0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1058 users visited in the last hour