Software for genomic island identification

Question

[RZanini]

hello , some tips for alternative software to identification genomic islands, besides islandviewer and Gohtam ? Or what the most reliable desktop software for identifying horizontal transfer ? Thank you

[RZanini]

Thank you so much Natasha! I'll try to use all to compare the results. best regards

Answer 1

[natasha.sernova]

These ones, but both from 2012.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302003/

GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030848

PIPS: Pathogenicity Island Prediction Software

http://molbiol-tools.ca/Genomics.htm

Several tools, like this one:

PAIDB v2.0

http://www.paidb.re.kr/about_paidb.php

Other two:

http://www.pathogenomics.sfu.ca/islandviewer/

The same, updated one

http://www.pathogenomics.sfu.ca/islandviewer/resources/

One more multiple tool:

Genomic island prediction software tools | Annotation

Genomic software tools and databases > Genome annotation databases and software tools

https://omictools.com/genomic-islands-category

Concerning horizontal gene transfer, see the following papers:

Automatic and accurate identification of integrons and cassette arrays in bacterial genomes reveals unexpected patterns

http://biorxiv.org/content/biorxiv/early/2015/11/09/030866.full.pdf

Identification and analysis of integrons and cassette arrays in bacterial genomes

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889954/