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GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences
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 gene...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302003/ https://www.ncbi.nlm.nih.gov/pubmed/22419842 http://dx.doi.org/10.6026/97320630008203 |
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author | Hasan, Mohammad Shabbir Liu, Qi Wang, Han Fazekas, John Chen, Bernard Che, Dongsheng |
author_facet | Hasan, Mohammad Shabbir Liu, Qi Wang, Han Fazekas, John Chen, Bernard Che, Dongsheng |
author_sort | Hasan, Mohammad Shabbir |
collection | PubMed |
description | 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: The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST |
format | Online Article Text |
id | pubmed-3302003 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
spelling | pubmed-33020032012-03-14 GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences Hasan, Mohammad Shabbir Liu, Qi Wang, Han Fazekas, John Chen, Bernard Che, Dongsheng Bioinformation Software 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: The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST Biomedical Informatics 2012-02-28 /pmc/articles/PMC3302003/ /pubmed/22419842 http://dx.doi.org/10.6026/97320630008203 Text en © 2012 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited. |
spellingShingle | Software Hasan, Mohammad Shabbir Liu, Qi Wang, Han Fazekas, John Chen, Bernard Che, Dongsheng GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences |
title | GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences |
title_full | GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences |
title_fullStr | GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences |
title_full_unstemmed | GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences |
title_short | GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences |
title_sort | gist: genomic island suite of tools for predicting genomic islands in genomic sequences |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302003/ https://www.ncbi.nlm.nih.gov/pubmed/22419842 http://dx.doi.org/10.6026/97320630008203 |
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