Genomic Island Hunter (GIHunter)

Transcription

1 2013 Genomic Island Hunter (GIHunter) Han Wang, Dongsheng Che Department of Computer Science East Stroudsburg University

2 Contents 1. Requirements 2 2. Installation Download GIHunter Extract GIHunter Compile GIHunter 3 3. Tutorial Program command Inputs Output A running example 5

3 1. Requirements Linux operating System is highly recommended. GIHunter was written in C++, and was tested on Ubuntu systems. Java SDK v1.5 or higher. JDK can be downloaded from Perl 5.8.x, or higher. Perl can be downloaded from

4 2. Installation 2.1 Download GIHunter Download the GIHunter package from: Extract GIHunter Extract package by using the following command: (Suppose you have downloaded the package under the folder of desktop) > cd desktop > tar xvfz GIHunter.tgz...watch files unpacking... > cd GIHunter The distribution contains: GIHunter_Manual The description file about how to run GIHunter program Source Directory that includes all source codes Genome_inputs Directory of sample input data Genome_ouputs Directory of outputs GIHunter The executable file used to run GIHunter makefile The file used for compiling source code 2.3 Compile GIHunter To compile the program, type > make

5 3. Tutorial 3.1 Program command GIHunter takes four arguments for each genome. The first three arguments are input genome files, and the last one is the output folder. The general format is as follows:./gihunter <input1> <input2> <input3> <output> 3.2 Inputs The three input genome files should meet the following requirements: They are downloaded from the National Center for Biotechnology Information (NCBI) FTP server (ftp://ftp.ncbi.nih.gov/genomes/bacteria); They are: 1) FASTA Format DNA sequence file (.fna); 2) Protein Table file (.ptt); and 3) RNA table file (.rnt) in that oder; Three input files in the arguments must be from the same genome. e.g. NC_ fna, NC_ ptt, NC_ rnt 3.3 Output Under the folder of Genome_outputs, a subfolder given in the command argument will be created. This subfolder name should be provided corresponding to input genome files, so the same subfolder name may be created. For instance, if the fourth argument is given as NC_000913, then subfolder of NC_ under Genome_outputs will be created, i.e. Genome_outputs/NC_ A final predicted genomic island location results will be saved in the subfolder, with the name of outputfile_gis.txt, depending on output file name (i.e., genome name). e.g., NC_000913_GIs.txt Each line in the output file contains two numbers, representing the start location and stop location of the predicted GI in the genomic sequence.

6 3.4 A running example Go to GIHunter folder. e.g. >cd ~/Desktop/GIHunter/ Make sure that minimum requirements are met, i.e., Linux and java & perl installed. Compile the program using make Type the following command (one line):./gihunter Genome_inputs/NC_ fna Genome_inputs/NC_ ptt Genome_inputs/NC_ rnt NC_ The predicted results will be saved in Genome_outputs/NC_000913, with the name of NC_000913_GIs.txt. The following shows the part of predicted results There is another folder GIV, which contains the files that are used for generating GI images.