Genome Visualizer

LED Flow is a Quartz Composer visualizer plugin for iTunes. This Quartz Composer Composition is a challenge to visualize the flow of music. A real level meter is usually fixed. But in this case, it is floating on the music. Platforms: Mac, iTunes 8.0.1 or later

LineReaction is a Quartz Composer visualizer plugin for iTunes. The sound flows like the waveform. Platforms: Mac

Figure is a Quartz Composer visualizer plugin for iTunes. It goes slowly between jacket image and title. Platforms: Mac

Bugaboo is a Quartz Composer visualizer plugin for iTunes. Living thing of light shakes like a dance,reacting on the sound. Platforms: Mac

A Quartz Composer iTunes Music Visualizer utilizing Apple's Cover Flow concept within iTunes What's new in this version: * Implement trackball or mouse movements with mouse-down to move animated covers around when present. Platforms: Mac

An iTunes Visualizer using Leopard's Quartz Composer of album cover art displayed on rotating cubes of various opacity. Platforms: Mac

aSTARick is a wildly customizable iTunes music visualizer. After installing just press "h" to bring up some handy help. Installation: 1. Decide if you want to install for all users, or just yourself (this may depend on your access permissions). If you want to install for all users the... Platforms: Mac

dbSNPtool starts a GUI to return polymorphism data from dbSNPwww.ncbi.nih.gov/SNP Calling dbsnptool start the GUI, SNP % records are returned based on keyword. Each result is presented in a % listbox, clicking on the entry loads the sequence into the sequence %viewer. Information is presenting... 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

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description... Platforms: Matlab

NanoVis (beta version) allows to visualize any atomistic structure by reading a user defined file. The supported formats are "gen" and "xyz". There are two display modes: normal and "spacefill". In the zip file, with the .m file, there are two examples of structure and a file containing the atoms... Platforms: Matlab

The BLAST Ring Image Generator (BRIG) is a cross-platform JAVA application, it has a graphical user interface, which takes the user step-by-step through the configuration of a genome circular visualization. Platforms: Mac

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the... Platforms: Mac

bedtools: a flexible suite of utilities for comparing genomic features. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.... Platforms: Mac

JDSA is a Java program that will degenerately search DNA sequences. This program searches sequences for multiple nucleotides at a given position (positional degeneracy), limited overall sequence accuracy (group degeneracy) or variable spacing between multiple DNA sequences (spacing degeneracy).... Platforms: Mac

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies This tool aims to identifying structural variations with both clustering and... Platforms: *nix

GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of intensity data. It is powerful and sensitive in detecting small CNV associations, and retains high power for large CNVs. Platforms: *nix

Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly. Platforms: *nix

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human... Platforms: *nix

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Cross-Platform: Molecular... Platforms: *nix