I want to identify core genome among approximately 70 strains of a species of bacteria whose genomes are completed. Any one among them can be considered as a reference over the remaining strains. I want to identify the highly conserved proteins among the strains.
There are a variety of ways of approaching this question. Not the least of which is how you define the "core" genome. However if you want a pre-made pipeline to go from fasta or .gbk files to identifying a core amongst other things and that uses simple command line input in a linux system try "Get homologues". See the article "GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis", and decide if that is what you want.
If you are more into graphical approach that also allows to create a phylogenetic tree, Venn diagrams and more, you might want to have a look at EDGAR:
https://edgar.computational.bio.uni-giessen.de/cgi-bin/edgar_login.cgi
There are a number of open projects, but you can also request a private project that only selected people can access and in which genomes of your choice are loaded.
Thank you Barbara and Christian, but I am a bit week at linux and will try GET_HOMOLOGUES. But dear Christian EDGAR is not leaving me to create an account. its showing errors.Kindly help.
As stated under "News" you have to request an account if you want to get a private project, you cannot create one yourself. Just click on "contact" (small link directly above the big "LOGOUT" button). That should open up a mail window to the guy who develops EDGAR.
But try browsing one of the open projects first to see whether EDGAR is what you need.
Dear Christian, Thank you for your kind reply. Yeah I have submitted a request for the use of an account at EDGAR. Parallelly I was able to use the see the results as a guest (which was not able at to be done at last time). Now my query is regarding identification of a core genome among all the 70 pathogens at once. In EDGAR, with the core genome option, I can consider only one over several contigs and not many over all. I also saw the Venn diagram option, which is exactly I am in need, but this also has a limitation which is obvious, and is one cant choose more then 5 contigs. So how can be this solved ?
Dear Sandeep
In addition to EDGAR, you can test other online tools that can calculate core and pan-genome such as:
http://pangp.big.ac.cn/
or
http://cge.cbs.dtu.dk/services/PanFunPro/
or
https://lfz.corefacility.ca/panseq/analyses/
Wish you good luck!
I'd suggest Hamstr (http://www.deep-phylogeny.org/hamstr/) or OrthoMCL (http://www.orthomcl.org/orthomcl/).
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