Genome comparison tool

Question

[natasha]

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

Answer 1

[natasha.sernova]

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://www.researchgate.net/publication/269115957_Identifying_Pathogenicity_Islands_in_Bacterial_Pathogenomics_Using_Computational_Approaches

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

book_phages

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/

A: Genome comparison tool

[natasha]

Thank you, this is really helpful