Tag: Genomic Island

GIPSy 1.1.3 – Genomic Island Prediction Software

GIPSy 1.1.3

:: DESCRIPTION

GIPSy extends on the PIPS idea and implements a software for using genomic features to predict pathogenicity islands as well metabolic and resistance islands in bacterial genomes.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

GIPSy

:: MORE INFORMATION

Citation

J Biotechnol. 2016 Aug 20;232:2-11. doi: 10.1016/j.jbiotec.2015.09.008. Epub 2015 Sep 12.
GIPSy: Genomic island prediction software.
Soares SC, Geyik H, Ramos RT, de Sá PH, Barbosa EG, Baumbach J, Figueiredo HC, Miyoshi A, Tauch A, Silva A, Azevedo V.

LiSSI 1.0 – Integrated Bioinformatics Platform for Genomic Island Analysis

LiSSI 1.0

:: DESCRIPTION

LiSSI (Life-Style-Specific-Islands) is a java tool for predicting life-style-specific genomic islands through evolutionary conservation. It is divided into three sequentially executed modules: evolutionary sequence analysis, island detection, and machine learning.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

LiSSI

:: MORE INFORMATION

Citation

J Integr Bioinform. 2017 Jul 5;14(2). pii: /j/jib.2017.14.issue-2/jib-2017-0010/jib-2017-0010.xml. doi: 10.1515/jib-2017-0010.
LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.
Barbosa E, Röttger R, Hauschild AC, de Castro Soares S, Böcker S, Azevedo V, Baumbach J.

COLOMBO 4.0 / SIGI-HMM – Statistical Analysis of Sequences of a Genome /Prediction of Genomic Islands in Prokaryotic Genomes

COLOMBO 4.0

:: DESCRIPTION

COLOMBO is a software framework equipped with a GUI for the statistical analysis of sequences of a genome. It can be equipped with different plugins that actually perform the analysis. The current version of COLOMBO is supplied with SIGI-HMM, a tool for the prediction of Genomic Islands.

::DEVELOPER

Theoretical Computer Science and Algorithmic Methods , at the University of Göttingen.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • Perl

:: DOWNLOAD

COLOMBO

:: MORE INFORMATION

Citation

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R.
BMC Bioinformatics. 2006 Mar 16;7:142.

IGIPT – Integrated Genomic Island Prediction Tool

IGIPT

:: DESCRIPTION

IGIPT is a web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region.

::DEVELOPER

Dr.Nita Parekh, Ruchi Jain , Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology – Hyderabad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IGIPT

:: MORE INFORMATION

Citation

IGIPT – Integrated genomic island prediction tool.
Jain R, Ramineni S, Parekh N.
Bioinformation. 2011;7(6):307-10. Epub 2011 Nov 20.