Tag: Gain

GLOOME 201305 – Gain Loss Mapping Engine

GLOOME 201305

:: DESCRIPTION

The main purpose of GLOOME server is to accurately infers branch specific and site specific gain and loss events.

:: DEVELOPER

Edmond J. Safra Center for Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GLOOME

:: MORE INFORMATION

Citation:

Genome Biol Evol. 2011;3:1265-75. doi: 10.1093/gbe/evr101. Epub 2011 Oct 4.
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony–a simulation study.
Cohen O1, Pupko T.

GLOOME: gain loss mapping engine.
Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T.
Bioinformatics. 2010 Nov 15;26(22):2914-5. doi: 10.1093/bioinformatics/btq549.

GISTIC 2.0.23 – Detect Regions of Significant Copy-number Gains and Losses

GISTIC 2.0.23

:: DESCRIPTION

GISTIC  (Genomic Identification of Significant Targets in Cancer) facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISTIC

:: MORE INFORMATION

Citation

Genome Biol. 2011;12(4):R41. Epub 2011 Apr 28.
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G.

GAIN 0.2.0 – Genetic Association Interaction Network tool

GAIN 0.2.0

:: DESCRIPTION

GAIN is based on interaction information between three attributes; in this case, between two single nucleotide polymporphisms (SNPs) and a class or phenotype attribute. Interaction information is the gain in phenotype information obtained by considering SNP A and SNP B jointly beyond the phenotype information that would be gained by considering SNPs A and B independently.

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 GAIN

:: MORE INFORMATION

Citation

PLoS Genet. 2009 Mar;5(3):e1000432. doi: 10.1371/journal.pgen.1000432. Epub 2009 Mar 20.
Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis.
McKinney BA1, Crowe JE, Guo J, Tian D.