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3D-PSSM Internet Browser  Windows
Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit).
Web Site Home Web Site: Biomolecular Modelling Laboratory

AGADIR Internet Browser
An algorithm to predict the helical content of peptides.
Web Site Home Web Site: EMBL

Abalone Windows
a program for biomolecular modeling. General Features: Molecular Dynamics, optimization, implicit and explicit water.
Web Site Home Web Site: Agile Molecule

Antheprot 2.9 MS-DOS  Unix  Windows
This is a protein sequence analysis package.
Web Site Home Web Site: Institut de Biologie et Chimie des Proteines

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

BCM PSSP Internet Browser
Protein secondary structure prediction using a variety of algorithms.
Web Site Home Web Site: Baylor College of Medicine

BioMedCAChe Linux  Mac  Unix  Windows
BioMedCAChe is a new computer-aided chemistry software package designed specifically for bio- and medicinal chemists. It provides powerful software tools to accelerate the drug discovery process. BioMedCAChe enables to analyze protein sequences and optimize their 3D structures, build protein structures by homology, dock ligands, and model enzyme reactions using whole enzymes.
Web Site Home Web Site: BioMedCAChe - Software for bio and medicinal Chemists

CAChe Linux  Mac  Unix  Windows
CAChe is a leading computer-aided chemistry modelling package designed for experimental chemists conducting research in life science, materials and chemical, as well as for undergraduate and graduate educators. CAChe lets every chemist visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compounds with an easy-to-use, award-winning interface on desktop computers.
Web Site Home Web Site: Use CAChe to model your experiments

CLC Combined Workbench Linux  Mac  Windows
CLC Combined Workbench 1.0 aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Protein family analysis (PFAM) - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, SwissProt, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Protein Workbench Linux  Mac  Windows
CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CPHmodels Internet Browser
CPHmodels is a collection of methods and databases developed to predict protein structures. It currently consists of the following tools: CPHmodels: predicts protein structure using comparative (homology) modelling; distanceP: A neural network based method to predict contacts between C-alpha atoms from the amino acid sequence (formerly Sowhat); RedHom: A tool to find a subset with low sequence similarity in a database.
Web Site Home Web Site: CBS, Technical University of Denmark

DICROPROT MS-DOS  Windows
A package of methods designed for the estimation of protein sequence secondary structure
Web Site Home Web Site: PBIL

DSC Internet Browser
Discrimination of Protein Secondary Structure Class. Produces multiple alignment to predict secondary structure.
Web Site Home Web Site: Biomolecular Modelling Laboratory

Dr.T.DHANABAL 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

Expression Windows
Expression is a revolutionary new application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. Expression uses the very latest computing technology to set new standards in the way sequences are analysed. Features include: Sequence Annotation,Graphical Sequence Map, Degenerate DNA and Amino Acid Sequence Support, Restriction Analysis, Primer Design and Analysis, ORF Prediction, Pattern Finding, Reverse Translation, GenBank Searching, Pattern and Motif Identification, Multiple Sequence Alignment, and Protein Structure Prediction.
Web Site Home Web Site: Genamics

FAST MS-DOS
FAST is a package designed to study protein structure by drawing profiles of specific amino acid parameters.
Download  (140 kb, 26-Jan-1990)

FlexX Internet Browser  Unix
Program for predicting complex structures of proteins with small ligand molecules such as inhibitors or substrates under consideration of the ligand's conformational flexibility. Fast computation times (about 2min/complex) allows the application in virtual screening scenarios.
Web Site Home Web Site: GMD (German National Research Center for Information Technology)

Ftrees Windows
Feature Trees is a new kind of descriptor for molecular similarity and diversity analysis. Instead of a linear representation of a molecule like a bitstring or a vector, the molecule is described by a tree structure representing its major chemical building blocks and the way they are connected. In order to compare two molecules, highly efficient mapping algorithms are used to generate a matching between groups of molecule with similar steric and chemical properties.
Web Site Home Web Site: GMD (German National Research Center for Information Technology)

GENtle Windows
GENtle is a program for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, specialized calculators, PCR, gel image display, virtual gel simulation, and more.

GORIV Internet Browser
Secondary structure prediction of proteins using the GORIV (Garnier et al.) method.
Web Site Home Web Site: PBIL

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™

HMMTOP Internet Browser
HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins
Web Site Home Web Site: Hungarian Academy of Sciences

HNN Internet Browser
Secondary structure prediction of proteins using Hierarchial Neural Network approach.
Web Site Home Web Site: PBIL

HTH 1.0.5 MS-DOS  Unix
Prediction of helix-turn-helix regions in protein sequences. Requires C compiler.
Download  (12 kb, 04-Jan-1994)

HTH 1.0.5 (Mac) Mac
Prediction of helix-turn-helix regions in protein sequences. Requires C compiler.
Download  (62 kb, 04-Jan-1994)

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