Dapple 0.88pre4 – DNA Microarrays Image Analysis

Dapple 0.88pre4

:: DESCRIPTION

Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities.

Dapple is designed to work with microarrays on glass. The spot-finding techniques used are robust to uneven spot sizes and positional deviations caused by “wobbling” of the arraying robot, as well as image noise and artifacts. As long as your spots are consistently circular, Dapple has a good chance of finding them accurately.

::DEVELOPER

Jeremy Buhler

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Dapple

:: MORE INFORMATION

Citation:

J. Buhler, T. Ideker, D. Haynor, “Dapple: Improved Techniques for Finding Spots on DNA Microarrays”, University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-2000-08-05, (2000)  Supplement.

DAPPLE 2 – Homology-based Prediction of Phosphorylation Sites

DAPPLE 2

:: DESCRIPTION

DAPPLE is a homology-based method for predicting phosphorylation sites in an organism of interest. It uses BLAST searches of experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylation sites in an organism of interest. It outputs a table containing information helpful for choosing phosphorylation sites that are of interest to you, such as the number of sequence differences between the query site and the hit site, the location of the query site and the hit site in their respective intact proteins, and whether the corresponding intact proteins are reciprocal BLAST hits (and thus predicted orthologues).

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DAPPLE 2: a tool for the homology-based prediction of post-translational modification sites.
Trost B, Maleki F, Kusalik A, Napper S.
J Proteome Res. 2016 Jul 1.

Bioinformatics. 2013 Jul 1;29(13):1693-5. doi: 10.1093/bioinformatics/btt265. Epub 2013 May 8.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.
Trost B, Arsenault R, Griebel P, Napper S, Kusalik A.

DAPPLE 2.0 – Disease Association Protein-Protein Link Evaluator

DAPPLE 2.0

:: DESCRIPTION

DAPPLE looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature. The hypothesis behind DAPPLE is that causal genetic variation affects a limited set of underlying mechanisms that are detectable by protein-protein interactions.

::DEVELOPER

DAPPLE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tartar D, IIBDGC, Cotsapas C, Daly MJ. 2011
Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology.
PLoS Genetics 7(1): e1001273