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