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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...

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Detalles Bibliográficos
Autores principales: Hasan, Mohammad Shabbir, Liu, Qi, Wang, Han, Fazekas, John, Chen, Bernard, Che, Dongsheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2012
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
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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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