Hi
I have annotated a series of bacterial isolates using prokka, and am now wondering what are the best methods to explore and compare these annotations. I know that I can search for virulence factors within these annotations. However, are there any tools available to search for pathogenicity islands or phages?
Thanks
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written
by
natasha
1 answer
There are a lot of such tools.
Tools to search for pathogenicity islands or phages in bacterial genomes:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235732/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC321463/ - 2004, clinical tools
http://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2006.00794.x/full
https://microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-3-2
http://www.nature.com.sci-hub.cc/nrmicro/journal/v8/n5/full/nrmicro2350.html
http://www.nature.com/articles/srep12561
http://molbiol-tools.ca/Genomics.htm
Methods to explore and compare bacterial annotations:
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1826-4
http://www.hindawi.com/journals/abi/2015/635437/
https://holtlab.net/2015/02/25/tools-for-bacterial-comparative-genomics/
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