About GIST

Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs has a significant role in biomedical research to describe special characteristics present in some bacteria but absent in their ancestors. The purpose of developing the software package, Genomic Island Suite of Tools (GIST), is to provide a platform for scientific users to predict GIs using different programs. This software package includes five commonly used tools for genomic island prediction, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program known as EGID to ensemble the result of existing tools for a better prediction. These tools in GIST can be used either separately or sequentially. We also include a downloadable feature that facilitates collecting the input genomes automatically from the FTP server of the National Center for Biotechnology Information (NCBI). GIST was implemented in Java, and was compiled and executed on Linux operating systems.

Software availability



Disclaimer: this software is free to use, modify, redistribute without any restrictions.

Documentation

To view PDF click here

Reference

Mohammad Shabbir Hasan, Qi Liu, Han Wang, John Fazekas, Bernard Chen, and Dongsheng Che. GIST: Genomic Island Suite of Tools for predicting genomic islands in genomic sequences, submitted.

Dongsheng Che, Shabbir Hasan, Han Wang, John Fazekas, Bernard Chen and Xiuping Tao - M Are Better Than One: An Ensemble Method For Genomic Island Prediction. Proceedings of the 6th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2012).

Contact

Bugs, problems, suggestions can be reached to
Dongsheng Che: dche@po-box.esu.edu


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Page last updated: Feb. 2, 2012