Comparative Anatomy

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.

We attempt to reproduce and efficiently implement in MATLAB publicly available methods of Affymetrix MAS 5 and GCOS 1.2 software that perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files and create corresponding CHP data structures:1. CHP data structure is...

CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication: Pierstorff, N., C.M. Bergman &...


Platforms: Mac, BSD

GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.


Platforms: Windows, Mac, Linux

Run "parrecreader.m"This program reads the native PAR/REC files, imports them to Matlab workspace and displays them.This is a stripped down version of code developed for MR Elastography purposes, but should be useful for other applications as well.Two sample datasets are included: i)T2W anatomy...


Platforms: Matlab

ProDy is a Python package designed for protein structural dynamics analysis. ProDy is developed by Ahmet Bakan and licensed under the GPLv3. New features and functions are constantly being added to ProDy. The following are the main features that are present and working fine: Protein structure...


Platforms: Mac

GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and...


Platforms: Mac

Java Micro Benchmark - control tasks required to determine the comparative performance characteristics of the computer system on different platforms. Can be used to determine the effect of different software on the performance of a computer system.


Platforms: Windows, Mac, Linux

This tool enhances signal detection for broad-mass TOF spectra by accounting for changing peak width and providing peak-shape-dependent filtering capabilities. A set of input TOF spectra is processed to produce aligned peak list and array of corresponding signal intensities. Signal processing...


Platforms: Matlab

MCGH is a Matlab toolbox with graphical interface to analysis DNA microarray-based comparative genomic hybridization (CGH) experiments. CGH on DNA microarray enable us to measure the copy numbers of thousands of genes through the genome. M-CGH allows us to visualize the copy number changes...


Platforms: Matlab

This package includes a number of methods of determining the delay between two period signals. The delay may be calculated to subsample accuracy. Methods include: three-point interpolation using parabolic, Gaussian, or cosine functions; a phase method; and an iterative method.A simple example is...


Platforms: Matlab