IslandPath-DIMOB is a standalone software to predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes.
Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest.
This version here is a modification of the original version (https://github.com/brinkmanlab/islandpath) that allows IslandPath-DIMOB to process assembly draft genomes in multiple contigs and not using a reference genome.
Although the original version has multiple instalation options: docker, github releases... for this particular version we would only rely on github clone.
Clone the latest code from github:
git clone https://github.com/JFsanchezherrero/islandpath
Dependencies
No additional dependencies were added to this new implementation. IslandPath-DIMOB remains with the same original dependencies.
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Though IslandPath-DIMOB should work with any OS, it has only been tested with linux.
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Perl version 5.18.x or higher
The latest version of Perl can be obtained from http://www.cpan.org -
The following Perl libraries are also required:
- Data::Dumper
- Log:Log4perl
- Config::Simple
- Moose
- MooseX::Singleton
- Bio::Perl
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A working installation of HMMER3
HMMER can be obtained from http://hmmer.org/
"hmmscan" must be within your executable path.
IslandPath-DIMOB v1.0.1_b takes as input an annotated complete/draft genome as a genbank (.gbk) or an embl (.embl) file.
perl Dimob.pl <genome.gbk> <output_name> [cutoff_dinuc_bias] [min_length]
Default values:
cutoff_dinuc_bias = 8
min_length = 8000
Example:
perl Dimob.pl example/NC_003210.gbk NC_003210_GIs
perl Dimob.pl example/NC_003210.gbk NC_003210_GIs 6 10000
perl Dimob.pl example/NC_000913.embl NC_000913_GIs 6 10000
Bertelli and Brinkman, 2018
Hsiao et al., 2005
Email [email protected] (contact person: Claire Bertelli) for the original version.
Email [email protected] (contact person: Jose F. Sanchez-Herrero) or via github issue for the modification version.
IslandPath-DIMOB is distributed under the GNU General Public License. See also the LICENSE file included with this package.
Give credit to the original version of this software available at https://github.com/brinkmanlab/islandpath
Several new implementations were performed in order to add multicontig functionality.
We additionally fix some bugs and warning messages:
- Fix smartmacth experimental warning message
- Fix dinuc bias loop iteration bug brinkmanlab#8 (comment)
We increase the input and output options
- Use GI min_length as a variable
- Use cutoff_genes_dinuc as a variable
- Output csv information for dinucleotide bias.
- Provide additional information such as annotation of the genes within each GI
Increased recall and precision in the prediction of genomic islands based on the presence of dinucleotide bias and mobility genes. Standardization of input file types, and automatic generation of the other file types required by IslandPath-DIMOB.
Input: gbk or embl file
Publication: Bertelli and Brinkman, 2018
Improvement and assessment of IslandPath-DIMOB predictions by Morgan Langille
Input files: ffn, faa, ptt
Publication: Langille et al., 2008
Second version developed by Will Hsiao
Further studies used dinucleotide sequence composition bias and the presence of mobility genes to develop a data set of GIs (IslandPath DIMOB) for multiple organisms and revealed that these genomic regions contain higher proportions of novel genes.
Input files: ffn, faa, ptt
Publication: Hsiao et al., 2005
IslandPath-DINUC developed by Will Hsiao
IslandPath was originally designed to aid to the identification of prokaryotic genomics islands (GIs), by visualizing several common characteristics of GIs such as abnormal sequence composition or the presence of genes that functionally related to mobile elements (termed mobility genes).
Publication: Hsiao et al., 2003
IslandPath-DIMOB was written and updated by several members of the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada
2015 - present: Claire Bertelli [email protected]
2009 - 2015: Matthew Laird [email protected]
2007 - 2009: Morgan Langille [email protected]
2003 - 2007: Will Hsiao [email protected]