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Ascalaph Linux  Windows
Molecular Modelling Suite. * Molecular Design * Molecular mechanics simulations * Quantum calculations * Force Field development * GPU accelerated Molecular Dynamics
Web Site Home Web Site: Agile Molecule

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

CLC RNA Workbench Linux  Mac  Windows
CLC RNA Workbench aggregates a large number of advanced RNA sequence analyses and other bioinformatics analyses in one single, integrated, user-friendly, and intuitive software application. Some features are Secondary RNA structure prediction, Graphical view and editing of secondary RNA structures, Tabular view of RNA structures and RNA energy contributions, Symbolic representation of RNAs in sequence view, Pattern search, Search for sequence matches, Motif search for basic patterns, Motif search using regular expressions, Motif search with ProSite patterns, Pattern discovery (unknown patterns), Project and data management, Detailed history log, All types of files can be saved in local projects, and launched from the program, DNA, RNA and protein sequence editor displaying both linear and circular molecules, Multiple alignment of DNA, RNA, and proteins: ClustalW, Muscle, T-Coffee, MAFFT, Kalign. Interactive logo graphs along both DNA, RNA and Protein alignments, BLAST, and much more.
Web Site Home Web Site: www.clcbio.com

Chromatogram Explorer-Exploring and trimming your chromatograms is not a problem anymore Mac  Windows
Chromatogram Explorer is a very easy to use tool that will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. You can view the chromatograms while browsing through folders using its integrated Windows Explorer. Chromatogram Explorer can also trim low quality bases at the ends of your samples with a single push of a button! Now you can process/sort/search chromatograms in seconds.
Web Site Home Web Site: DNA Baser - Free biology software

Genetic MS-DOS  Windows
Web Site Home Web Site: www.arya.com

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.

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.

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™

IJARBS Windows
International Journal of Advanced Research in Biological Sciences publishes original papers, review articles, and short communications. The mission of International Journal of Current Research in Biological Sciences is to significantly broaden the knowledge base of its readers and in this sense; the journal shall focus on only those papers that fall within its scope. The scope of the journal encompasses research articles, original research reports, reviews, short communications and scientific commentaries in the fields of science and Agricultural sciences and medical science and other fields of basic and applied sciences. International Journal of Advanced Research in Biological Sciences aims to publishers various fields of biological sciences including Life sciences, Medical sciences, Microbiology, Biotechnology, Agricultural Sciences, Chemical Sciences, and Environmental Sciences, Botany, Plant Science, Biochemistry, Zoology, Marine Biology, Genetics, Molecular Biology, Pharmacogenomics, Pharmacology, Medicine and Dentistry, Veterinary Science, Anatomy, Nutrition and Metabolism, Cancer Research and Experimental Oncology, Clinical Pathology and Forensic, Medicine, Agricultural Engineering, Agricultural Biotechnology, Agricultural Microbiology and Plant Pathology.
Web Site Home Web Site: International Journal of Advanced Research in Biological Sciences

International Journal of Current Research in Chemistry and Pharmaceutical Sciences Internet Browser
International Journal of Current Research in Chemistry and Pharmaceutical Sciences (IJCRCPS) (p-ISSN:2348 - 5213; e-ISSN:2348-5221) is an International, Peer Reviewed, Indexed, Monthly, Online, Free Access Scientific Research Journal Published in monthly.IJCRCPS provide a platform to all researchers, academicians, scientists, person working in industries and others to share their information
Web Site Home Web Site: International Journal of Current Research in Chemistry and Pharmaceutical Sciences

Loop Viewer 1.0 Mac
Graphical representation of RNA folding.
Download  (130 kb, 06-Nov-1990)

MC-SYM searches the conformational space of RNA and generates models that are of atomic precision.
Web Site Home Web Site: University of Montreal

MOJ Proteomics & Bioinformatics Internet Browser
MedCrave Online Journal for Proteomics and Bioinformatics (MOJPB) is an internationally acclaimed, peer reviewed multi - dimensional journal which aims to provide top quality information in the proteomics and bioinformatics. The scope of bioinformatics is really huge in nature and thus, this journal covers all sorts of details in this field. MOJPB is proud to accept quality reviews, articles, manuscripts, rapid communications and editorials in this field which will be enlightening the scientific community.
Web Site Home Web Site: MOJ Proteomics & Bioinformatics

MulFold 2.0 Mac
Software for prediction of RNA secondary structure by free energy minimization.
Download  (205 kb, 06-Nov-1990)

Multiple RNA Sequence Alignment Unix
This program gives a proper RNA-sequence alignment, from which stem regions can be specified.
Web Site Home Web Site: ICOT

Computer Prediction of RNA Structure.
Download  (115 kb, 23-Oct-1989)

Primer Designs
PrimeSyn Lab Inc. is a recognized leader in the area of custom DNA synthesis and purification within the USA. PrimeSyn Lab also specializes in primer design, beacon design, protein analysis, mass spectral analysis, protein purification / characterization, analytical methods development, small molecule synthesis and analysis. PrimeSyn Lab’s provides products and services for contract research, product development and assay development within the Bio-pharmaceutical industry.
Web Site Home Web Site: PrimeSyn Lab Inc.

RNA structure prediction (15), and protein identification(41) Windows

RNAdraw Windows
An application that uses RNA optimal structure, basepair-probability matrix, and heat curve calculation to predict RNA structure.
Web Site Home Web Site: CABIOS

RNAdraw 1.1b2 Windows
Prediction and analysis of secondary structure of RNA. For Windows 95/98/NT.
Web Site Home Web Site: Ole Matzura Download  (283 kb, 22-Dec-1995)

Vienna RNA Package Unix
A package for RNA secondary structure prediction and comparison consisting of a code library and several stand-alone programs for prediction and comparison.
Web Site Home Web Site: Institut fuumlr theoretische Chemie

loopDloop Unix  Windows
loopDloop is a tool for drawing RNA secondary structures in molecular biology.
Web Site Home Web Site: IUBio

loopDloop (Mac) Mac
loopDloop is a tool for drawing RNA secondary structures in molecular biology.
Web Site Home Web Site: IUBio Download  (380 kb, 14-Aug-1992)

primer3 Windows

tRNA Search 1.0 Mac
Identification of tRNA genes and drawing of folded t-RNA structures, which can be printed.
Download  (210 kb, 10-Apr-1991)

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