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ALP Windows
Automated Linkage Preprocessor. Determines sizes of microsatellite fragments separated on an A.L.F. Sequencer (Pharmacia Biotech), removes stutter, performs genotyping and Mendelian checks, and formats data for Lathrop's Linkage Program Package.
Web Site Home Web Site: MRC Human Genetics Unit

AmiraMol Linux  Unix  Windows
Together with Amira 2.3, an object-oriented interactive system for 3D data visualization, the new extension AmiraMol has been released. AmiraMol adds advanced tools for the visualization of Molecules. It combines Amira's strong capabilities for 3D data visualization like hardware accelerated volume rendering with specific tools for molecular visualization and data analysis. AmiraMol is available for Windows, Linux, IRIX, HP-UX, and SunOS. To get more information or to download a free trial version of Amira please visit our website:
Web Site Home Web Site: AmiraMol

AutoGene Windows
AutoGene Microarray Image Analysis System (MAS) is the first and most powerful image analysis tool for high throughput gene expression microarray and high-density membrane data analysis. AutoGene was designed to fully automate image analysis and data quantification operations.
Web Site Home Web Site: BioDiscovery

BASS Unix
A software program for tracking, extracting, and base calling DNA sequencing gels.
Web Site Home Web Site: MIT Genome Center

BED MS-DOS
Base EDitor. Sequence editor with speaker feedback.
Download  (75 kb, 16-Dec-1992)

BLAST 2.0 Internet Browser  MS-DOS
A tool used to identify any potential homologies of a given DNA or protein sequence with those stored in GenBank.
Web Site Home Web Site: NCBI

BandScan Windows
Protein gel image acquisition, documentation and analysis.
Web Site Home Web Site: Glyko

Bandleader 3.0 Mac
Image processing and analysis of data from protein gel electrophoresis.
Download  (512 kb, 16-Oct-1997)

DIG - Analysis, Reporting, Intelligence Linux  Unix  Windows
DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month.
Web Site Home Web Site: DigDB

DNASIZE 1.0 MS-DOS
DNASIZE has been developed for estimating the size of DNA fragments or size of proteins/peptides from agarose or SDS-PAGE data. DNASIZE computes a standard curve from the standard data (eg. migration distance of markers band ofnown size).
Download  (60 kb, 04-May-1994)

DNAfrag 3.03 MS-DOS
This program is used in restriction mapping of DNA or sizing of proteins from agarose or SDS-PAGE gels. It calculates the size of restriction fragments or peptide bands on gels or autoradiograms if standards are run on the same gel.
Download  (33 kb, 30-Jan-1992)

Digiseq MS-DOS
Digiseq will permit rapid input of DNA sequence data using either the keyboard or the Graf/Bar 7, a digitizing device which enables entry of sequence data by touching each band on a DNA sequencing gel.
Download  (55 kb, 13-Feb-1990)

DoubleDigester 1.1b (Mac) Mac
DoubleDigester is a program designed to help you make graphical restriction maps from gel data. The manual is in postscript format.
Download  (2232 kb, 24-Mar-1993)

DoubleDigester 1.1b (Unix) Unix
DoubleDigester is a program designed to help you make graphical restriction maps from gel data. The manual is in postscript format.
Download  (5158 kb, 24-Mar-1993)

Gel 1.01 Mac
GEL takes a set of standard DNA fragment sizes and mobilities and predicts the sizes of unknown fragments.
Download  (208 kb, 15-Apr-1992)

Gel 1.1b MS-DOS
GEL takes a set of standard DNA fragment sizes and mobilities and predicts the sizes of unknown fragments.
Download  (110 kb, 13-Apr-1992)

GelFrag 1.4 Mac
Calculation of DNA restriction fragment sizes.
Download  (130 kb, 22-Sep-1989)

GelQuest Windows
Software for the analysis of DNA fingerprint data: AFLP, RFLP, tRFLP, RAPD. GelQuest imports trace data (FSA files) from automtic sequencers as well as images from slab gels. It performs peak detection, fragment sizing using size standard matching and binning (bins, superbins, hyperbins). Exports data as trace files, tab-delimited spread sheaths, 01 matrix, Nexus, Newick and other formats.
Web Site Home Web Site: GelQuest DNA Fingerprint Software

GelReader Mac
A color imaging and analysis tool that extracts information from digitized electrophoretic gel images, allowing manipulation of lanes and bands.
Web Site Home Web Site: NCSA

GelReader 2.03 Mac
Analysis of information from digitized electrophoretic gel images such as DNA fragments. Optimised for processors with an FPU.
Download  (260 kb, 18-Sep-1992)

GelReader 2.03 (no FPU) Mac
Analysis of information from digitized electrophoretic gel images such as DNA fragments. Optimised for processors without an FPU.
Download  (270 kb, 18-Sep-1992)

GelReader 2.03 Samples Mac
Analysis of information from digitized electrophoretic gel images such as DNA fragments. This file contains sample images for the GelReader only.
Download  (260 kb, 18-Sep-1992)

Genchek Linux  Mac  Unix  Windows

Genchek is a comprehensive, multi-platform, sequence analysis software package. It facilitates analysis of Expressed Sequence Tags (ESTs), Complete Genome, and SNP (Single Nucleotide Polymorphism) data. Genchek is a research information and experiment management tool that integrates public and proprietary data through a discovery workspace that provides contextual access to sequence analysis tools, content and services. Genchek has an integral database system that can be used to access, store, organize and retrieve DNA, protein and vector sequences in an intuitive environment that offers editing, management and annotation of sequences.

Web Site Home Web Site: Ocimum Biosolutions - BioIT - Bioinformatics - Genchek?

GeneSight Windows
GeneSight is used to mine the massive gene expression data generated from microarray technology. The result of microarray image analysis tools, such as BioDiscovery's ImaGene software, is a table of expression values for many thousands of genes under one or two conditions. GeneSight allows the researcher to select any number of such data tables, compare and explore this large database using many advanced visualization tools.
Web Site Home Web Site: BioDiscovery

Genowiz™ Linux  Mac  Windows

Genowiz™ is a powerful gene expression analysis program that has been designed to store, process and visualize gene expression data efficiently. It includes a suite of advanced analysis methods and allows researchers to select analysis methods appropriate for their dataset. Genowiz™ allows researchers to organize experimental information (MIAME), import data files quickly and easily, work with multiple experiments at the same time, import gene annotation files, preprocess and normalize data, perform cluster analysis, classify and view gene information, perform functional classification and track down intricate correlations in data by performing pathway analysis. All analysis done is tracked, saved into a database and can be retrieved at any point of time.

Data and Gene List Import
Genowiz™ supports a wide range of data formats pertaining to cDNA data and Affymetrix processed data. Users also have an option to upload data in customized formats. Customized uploader allows users to add and save new data formats. One-Click Uploader can then identify these formats.
Gene List files for annotating genes can also be imported.

MIAME
Minimum Information About a Microarray Experiment (MIAME) facilitates adoption of standards for microarray experiment annotation and data representation. Genowiz™ focuses on establishing standard microarray experimental data repositories and information sharing within the scientific community. Researchers can also exchange MIAME data by using MAGE ML document exchange format.

Data Transformation, Normalization and Filtration
In any type of expression analysis, pre-processing of data to reduce undesirable variation among datasets and to bring data to a common platform is a vital step. Genowiz™ provides users with a wide range of data transformation, normalization and filtration tools. These include:

• Data transformation options such as imputation of missing values, log transformations, mean/median, Z-transformation, subtract control, divide by control, scaling etc.
• Normalization techniques such as normalization for dye swap replicates, cDNA raw data normalization options (cDNA Loess and Print tip Loess) and quantile normalization. Separate normalization techniques are provided for cDNA and Affymetrix arrays. Normalization can be done using all genes or control genes.
• Filter data based on replicate genes, fold change, mean, standard deviation, calls and missing values. Replicate samples are handled using various parametric/non-parametric tests. Multiple testing correction can be applied to reduce false positives.

Data Analysis and Visualization
Genowiz™ comes equipped with several data analysis tools. Complete with excellent graphics, it is an excellent tool for interpretation of biologically meaningful results. Some of these tools include partition clustering, hierarchical clustering, SOM, PCA, gene shaving and discriminant PCA (for classification).

• Partition Clustering (k-means, Forgy's)
This tool classifies genes or samples in user-defined groups using distance parameters. The obtained clusters can be re-clustered. Re-clustering utility helps scientists pick a set of genes of their interest. A 2D PCA view shows the distribution of genes in various clusters.

• Hierarchical Clustering
One of the most important tools for studying relations between genes, this tool creates a dendrogram based on the relative distance between genes. The different optional parameters help the user in correctly determining the relationship between two genes. Models of analysis include single linkage, complete linkage and average linkage clustering. Genes, samples, or both together can be clustered.

• Self Organizing Maps
A two-way classification of genes into clusters based on novel artificial neural networks is an integral feature of data clustering tools in Genowiz™. This gives a deeper insight into clusters, as neighboring clusters are very similar to each other.

• Principal Component Analysis
This tool involves a mathematical procedure that transforms a number of (possibly) correlated variables into a (smaller) number of uncorrelated variables called principal components. These provide an insight into existent variability in the data.

• Gene Shaving
This method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other methods of gene expression analysis in that genes may belong to more than one cluster.

• Discriminant PCA
This statistical approach classifies samples of unknown classes based on training samples of known classes.

Biological Analysis
Genowiz™ annotates genes and classifies them into functional categories (Gene Ontology). Option of importing annotation files is also provided. Integrated pathways module aids researchers in understanding metabolic pathways in relation to expression data. Pathway maps edited/created can be associated with author details too. Coupled with biological information and gene ontological classification, it forms an excellent tool in understanding biological systems.

Utilities
Several utility options are present adding value to analysis performed:

Gene List Comparison: Subtle relations among datasets can be probed using this feature.
Pattern Simulation: An expression pattern can be defined and Genowiz™ lists out all genes with a similar expression pattern. This gene list can be saved and exported.
Gene Tracking: Important genes or genes of interest can be tagged and tracked throughout the analysis.

Web Site Home Web Site: Ocimum Biosolutions - BioIT - Bioinformatics - Genowiz™

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