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Old 07-24-2011, 02:13 AM   #1
Kalily101
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Default Genomic comparison

Hi everyone,
I wish to ask you a question about genomic comparison.
I"m currently working with Salmonella serovar Senftenberg. The genome of S. Senftenberg is not published, but I have a list of S. Senftenberg ORFs.
I wish to compare S. Senftenberg ORFs against all Salmonella enterica genomes (the site "ncbi blast" has the genomes of 1000 Salmonella serovars that can be downloaded as *.nsq file).
In the end I wish to understand the function of each gene in S. Senftenberg using this comparison.
How can I make this comparison, can you please recommend me of a useful program ?
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Old 07-24-2011, 03:57 AM   #2
bckirkup
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Default Ortholog finder

To do this procedure 'well' you can utilize OrthoMCL. For that, you will probably want all the Salmonella genomes (you may want some E. coli reference genomes as well); this way, you can cross-compare all the CDs and find the ones which are mutual best hits. Then you can transfer the best annotations within each family to your new CDs. Ones that are missing (ie in your genome, not the others) can be compared to other proteobacteria.
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Old 08-12-2011, 11:23 AM   #3
squidsnw
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Default orthomcl

Trying to get orthomcl to run actually. I'm on step 4 of 13 and its taking a long time. Currently, I'm running into the error of "Can't locate DBD/mysql.pm in @INC", and I'm not sure how to rectify this. I have mysql installed, and its working, and DBI and DBD databases are installed also... Any help would be much appreciated. Thanks!
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Old 08-27-2011, 03:49 AM   #4
bckirkup
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Default unsure

So, it has been a while since I ran orthomcl and I would hope that it has seen upgrades since then. Certain steps always did take ... a long time; even a very long time. So, don't be disheartened if something seems to be going slowly. As to test your install, I'd run it on two or three genomes first, just to make sure it will complete.

The developers have always been very responsive. You should ask them if you are running into a problem that is recurrent and show stopping.
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Old 08-28-2011, 08:22 AM   #5
SES
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Default

Quote:
Originally Posted by squidsnw View Post
Trying to get orthomcl to run actually. I'm on step 4 of 13 and its taking a long time. Currently, I'm running into the error of "Can't locate DBD/mysql.pm in @INC", and I'm not sure how to rectify this. I have mysql installed, and its working, and DBI and DBD databases are installed also... Any help would be much appreciated. Thanks!
OrthoMCL is trying to access the database and that access is provided by DBD::mysql. If you are getting a "Can't locate xxx in @INC" that means the module is not installed where Perl looks by default. You can modify the script to find the module if you ran Build for example, but did not install it. Try running the following command:

Code:
perl -MDBD::mysql -e 1
If it prints nothing then it is installed. If it prints "Can't find DBD/mysql.pm in @INC" then it is not installed.
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Old 09-01-2011, 05:37 AM   #6
squidsnw
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Default

I was actually able to rectify that error by moving the file into the lib perl was looking in. Thank you for your help. Now I am getting a different error. The orthomclInstallSchema program when properly run returns the following error.
"DBD::mysql initialisation failed: Can't locate object method "driver" via package "DBD::mysql" at /Library/Perl/5.10.0/darwin-thread-multi-2level/DBI.pm line 815, <F> line 14."
I'm not sure what this means as far as what is wrong with the running of the code, and any help would be most appreciated. Thanks!
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Old 09-01-2011, 05:40 AM   #7
SES
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You need to have DBI installed, then install DBD::mysql. Did you install these via CPAN or build them yourself?
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Old 09-01-2011, 06:47 AM   #8
squidsnw
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I installed it with CPAN.
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Old 09-01-2011, 06:53 AM   #9
SES
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Quote:
Originally Posted by squidsnw View Post
I installed it with CPAN.
Okay. Do you recall seeing any error messages about tests that failed?
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Old 09-01-2011, 07:05 AM   #10
SES
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Generally, there are a number of steps that I go through when I'm having trouble with a database. Is the server started? How you do this will vary depending on whether you installed MySQL from the installer or from MacPorts. Were the tables in the database populated, or was the data not loaded for some reason? You can check this from the mysql command line. Bear in mind that I have not used orthoMCL and I that I am just making suggestions. These type of errors are commonly related to the issues that I just mentioned or something to do with Perl, which is what it looks like. Or, it could be do to the script you are using and I can't really help you with that.
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Old 10-12-2011, 11:38 AM   #11
squidsnw
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So I was able to fix the overarching problem with the entire installation. I switched from a Mac to a Linux machine and the entire install process took about 3 hours. I'm still not sure why the Mac was unable to do it, but Linux definitely can and I am running the program now. Thank you very much for your help!
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Old 10-12-2011, 11:48 AM   #12
SES
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Awesome! Glad you got it to work. What you described is a general solution to problems I have had in the past. While it's interesting to try and make things work on a Mac it is sometimes counterproductive. Time is better spent analyzing data.
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