PET-Tool 3.0 – Processing the Sequences generated from PET technology

PET-Tool 3.0

:: DESCRIPTION

PET-Tool is a mySQL-based muti-component software package specifically designed for processing the sequences generated from PET (Paired-End diTag) technology.

:: DEVELOPER

the Cloning and Sequencing Group at the Genome Institute of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apach
  • MySQL
  • C Compiler

:: DOWNLOAD

 PET-Tool

:: MORE INFORMATION

Citation

Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Ken Sung, Yijun Ruan (2006)
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
BMC Bioinformatics 7, 390

MAXIT 8.120 – An application for Processing and Annotating of Macromolecular Structure data

MAXIT 8.120

:: DESCRIPTION

The Maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data.

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAXIT, Source Code

:: MORE INFORMATION

JESAM 0.8.1 – Parallel Processing DNA Sequence Comparison and Clustering

JESAM 0.8.1

:: DESCRIPTION

JESAM is a software components to create and publish EST alignments and clusters.

::DEVELOPER

Jeremy Parsons

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  JESAM

:: MORE INFORMATION

Citation

Bioinformatics. 2000 Apr;16(4):313-25.
JESAM: CORBA software components to create and publish EST alignments and clusters.
Parsons JD, Rodriguez-Tomé P.

Tool for Biomedical Image Processing & Detection of Cancer using ANN

Biomedical Image Processing & Detection of Cancer

:: DESCRIPTION

 An automatic tool for prediction and classification of cancerous/non-cancerous squamosal cells using image processing and artificial neural networks (ANN). The ANN program is much more flexible and user friendly. It also optimizes number of hidden nodes itself based on the prediction accuracy. The neural network used here is a two layer neural networks and it uses standard back propagation algorithm. The first layer is use for detection of nucleus, cytoplasm and background of the image.Whereas the second layer is used to classify images into cancerous or non-cancerous based on three cellular features: size of nucleus, size of cytoplasm and ratio of nucleus/cytoplasm sizes. Using image processing techniques we extracted 15 features for selected pixel (using a mouse event program written in DOT NET framework) of an image over its 3×3 neighbouring matrix (using program written in MATLAB and C). These parameters are input to first layer of ANN.

::DEVELOPER

Project Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 Project

:: MORE INFORMATION

ExpressYourself – Microarray Data Processing Platform

ExpressYourself

:: DESCRIPTION

ExpressYourself is an interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  •  web serve
  • Perl

:: DOWNLOAD

 ExpressYourself

:: MORE INFORMATION

Citation:

NM Luscombe, TE Royce, P Bertone, N Echols, CE Horak, JT Chang, M Snyder, M Gerstein (2003).
ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic Acids Res 31:3477-82.