IslandCafe

IslandCafe, is genomic island prediction tool that utilizes sequence composition and functional information to identify genomic islands.

Example

First set the permissions for the file

sudo chmod 775 cafe
sudo chmod 775 cafe.out

To run program on example files

./cafe -phylo -genus bartonella -gbk example.gbk

Input

CAFE requires genome sequence and annotations to predict genomic islands. These can be provided as a single Genbank file.

./cafe [options] -gbk  genome.gbk

If the genome is not annotated then CAFE can identify marker genes for genomic island. This requires Prodigal and Hmmer be installed and included in path

./cafe [options] -annot genome.fna

To use the Phylogenetic module of CAFE, first download reference protein sequence files (.faa format) in faa folder. CAFE requires atleast five reference protein files for comparison. faa folder should only have reference protein sequence files, remove pre existing files in faa folder if not running on example genome. Phylogenetic module also requires that genus name be speciied using -genus option

./cafe [options] -phylo -genus [genus_name] -gbk genome.gbk

Note this requires BLAST version 2.6 or higher. Phylogenetic module also requires that users specify the name

Options

--help Print help and exit

--info Print program information and exit

--annot Annotate marker genes. This option is only required if the input file is in fasta format. This option requires prodigal and Hmmer be installed and in path

--Thres Provide segmentation, contiguous clustering and non contiguous clustering thresholds (range: 0-1. eg 0.8 0.99999 0.999)

--gbk Use genbank file as input

--phylo Use phylogenetic module. Genus must be specified for using phylogenetic module. (eg ./cafe -phylo -genus escherichia -gbk ecoli.gbk)

--genus Specify genus name of the input genome

--out Output file name

--verbose print on screen

--expert keep temporary files for user analyses

--visual Make a map of genomic islands (Requires CGView be installed and in path)

Output

CAFE outputs a tab separated text file. File with suffix CAFE.txt shows genomic island predictions. It has four columns showing genomic island id, start and end co-ordinates, and length of the genomic island.

Requirements

IslandCafe requires bioperl (Modules -- File::Copy Bio::SeqIO List::MoreUtils List::Util). The cafe.out file is compiled using gcc compiler

Note

This program has been tested on 64-bit machine and is intended for use on 64-bit computers