Title

Authors

Affiliation

¹Department of Computer Science, East Stroudsburg University, East Stroudsburg, PA 18301, USA; ²College of Life Science and Biotechnology, Tongji University, Shanghai, 200092, China; ³Department of Computer Science, University of Central Arkansas, Conway, AR, 72035, USA.

Email

dche@po-box.esu.edu;; *Corresponding author

Article Type

Software

Date

Received January 27, 2012; Accepted February 10, 2012; Published February 28, 2012

Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs plays a significant role in biomedical research since such align genomic regions usually contain important features, such as pathogenic genes. We have developed a use friendly graphic user interface, Genomic Island Suite of Tools (GIST), which is a platform for scientific users to predict GIs. This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction. The tools in GIST can be used either separately or sequentially. GIST also includes 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/Unix operating systems.

Availability

http://www5.esu.edu/cpsc/bioinfo/software/GIST

Keywords

Prokaryotic genomes; Genomic islands; Sequence analysis

Citation

Hasan et al. Bioinformation 8(4): 203-205 (2012)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.