LaneRuler 1.1 – Identify Lanes in Gel Image

LaneRuler 1.1

:: DESCRIPTION

LaneRuler will identify lanes in a gel image. The lanes on such gels may not be straight and parallel due to various reasons, and these deviations must be accounted for in order to accurately size the restriction fragments in each lane. In order to meet the high throughput requirements by the projects at the British Columbia Cancer Agency Genome Sciences Center (GSC), the software has capability to verify and correct its results automatically, and prompting for user inspection only for extremely abnormal cases. In validation testing using Bacterial Artificial Chromosome (BAC) clones, the automatic lane tracking results gave restriction fragment sizing results that are comparable to those from manually supervised lane tracking results, achieving sensitivity and specificity of restriction fragment identification exceeding 95%. The current conception of the program is able to successfully process 96% of the gels with no human intervention.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Java

:: DOWNLOAD

LaneRuler

:: MORE INFORMATION

Citation

Wong, R.T.F.; Flibotte, S.; Corbett, R.; Saeedi, P.; Jones, S.J.M.; Marra, M.A.; Schein, J.E.; Birol, I.; (2010 )
LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images
Automation Science and Engineering, IEEE Transactions Volume: 7 Issue:3 706 – 708

Cross Checker 2.91 – Genetic Fingerprint Gel Image Analysis

Cross Checker 2.91

:: DESCRIPTION

Cross Checker is developed for analysis of genetic fingerprints such as RFLP, RAPD and AFLP.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Cross Checker

:: MORE INFORMATION

BEADS 1.1.13 – Spot Detection on 2-D Gel Images

BEADS 1.1.13

:: DESCRIPTION

BEADS is a program for spot detection on 2-D gel images. It is based on an analogy with beads flowing uphill on the surface of the gel image and on the analysis of their paths

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ MacOsX / Linux

:: DOWNLOAD

BEADS

:: MORE INFORMATION

Citation

Proteomics. 2008 Dec;8(23-24):4914-8. doi: 10.1002/pmic.200800644.
A method based on bead flows for spot detection on 2-D gel images.
Langella O, Zivy M.

Flicker 0.87.2 – Compare 2D Gel Images

Flicker 0.87.2

:: DESCRIPTION

Flicker is an open source Java application for comparing 2D gel (or similar) images across the Internet or locally. It is possible to visually compare a user gel image with a SWISS-2DPAGE image and then select spots for identification with the Expasy SWISS-PROT protein ID database. It also has rudimentary manual quantification of spot data.

::DEVELOPER

Flicker Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

Flicker

:: MORE INFORMATION

Citation:

Comparing 2-D Electrophoretic Gels Across Internet Databases,
PF Lemkin, GC Thornwall, J Evans (2005)
“The Proteomics Handbook”, JM Walker (Ed), Humana Press Inc, Totowa, NJ, pp 279-305.

TopSpot 3.0 – Analysis of the Gel Image

TopSpot 3.0

:: DESCRIPTION

TOPSPOT is a software which has been developed for the purpose of analysing 2-dimensional electrophoretic imaging (2DE) of gels. It enables the user to obtain qualitative and quantitative gel data from gel images available in a BMP format or obtained using a scanner. The development of the program entailed close co-operation between two institutes in Berlin, where the 2-dimensional electrophoresis was carried out. As a result, the structure and function of TOPSPOT have been shaped by the requirements of the 2DE laboratory. Statistical comparisons of gel data and the construction of a 2DE database can be carried out using conventional statistical and database programs, since all relevant TOPSPOT gel data are available in the ASCII format.

::DEVELOPER

Algorithmus, Prehm Berlin

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

TopSpot

:: MORE INFORMATION

Citation:

Electrophoresis. 1996 Nov;17(11):1700-12.
High-performance human myocardial two-dimensional electrophoresis database: edition 1996.
Müller EC, Thiede B, Zimny-Arndt U, Scheler C, Prehm J, Müller-Werdan U, Wittmann-Liebold B, Otto A, Jungblut P.

TinyQuant v1.55 – Gel Image Analysis

TinyQuant v1.55

:: DESCRIPTION

TinyQuant is a miniature utility for gel image analysis. Useful for integrating densities of gel bands in 16 bit greyscale (PC or Mac format “.gel” or TIFF files) or 24 bit RGB TIFF images, and for converting these to 8 bit greyscale TIFFs. Also useful for generating optimised 8 bit greyscale images from 24 bit RGB scans.

::DEVELOPER

Iscove Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

TinyQuant

:: MORE INFORMATION