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2D Hunt Internet Browser
2-D Electrophoresis Finder provides an interface for searching 2D electrophoresis-related pages on the web, by keyword.
Web Site Home Web Site: Expasy

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

AACompSim Internet Browser
AACompSim is a tool which allows the comparison of the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry.
Web Site Home Web Site: Expasy

ABI to FASTA free converter Windows
This free tool will batch convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button. With this automatic converter you can convert hundreds or thousands of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON! ---------- No installation process is required.
Web Site Home Web Site: DNA Baser Contig Assembler

AGM Build Linux  Windows
A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules * Chains with predetermined conformations * Charges and atom types according to selected Force Field
Web Site Home Web Site: Agile Molecule

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

AlleleID 5
AlleleID designs real time PCR and microarray probes and primers for identifying strains and sequences from an alignment and for amplifying and detecting patterns across sequences. AlleleID has a built-in ClustalW alignment module which aligns the nucleotide sequences. You can choose to amplify and detect sequence specific or conserved regions from the mix. AlleleID supports TaqMan, molecular beacons, Fret, TaqMan MGB and Microarray probes. A distinguishing feature of AlleleID is the ability to design real time PCR primers and probes to spot and amplify exons/introns
Web Site Home Web Site: Premier Biosoft

AlleleID version 6 Mac  Windows
AlleleID the comprehensive primer design tool can now design mutation specific/mRNA specific or DNA specific MLPA probes that are compatible with Pamchip array.
Web Site Home Web Site: Premier Biosoft

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

Anemona Mac  Windows
ANEMONA.XLT is an EXCEL template for calculation of enzyme kinetic parameters by non-linear regression. Details in A. Hernández and M. T. Ruiz (1998) An EXCEL template for calculation of enzyme kinetic parameters by non-linear regression. Bioinformatics 14(2):227-228. Requires SOLVER ADD-IN installed in your copy of EXCEL.
Download  (198 kb, 06-Oct-1997)

Array Designer Linux  Mac
Array Designer is a high-throughput program for designing highly specific oligos for expression and SNP detection microarrays. The program has a unique homology avoidance algorithm that ensures high specificity. The sequences are BLASTed, the results are automatically interpreted and the most optimal oligos are designed avoiding regions of signinficant homology. The program enables BLAST search of the oligos designed. This feature helps in verifying their specificity. It is also possible to BLAST search sequences against all the databases available at NCBI for cross species studies. The design can be exported in a convenient spreadsheet format for ordering synthesis.conditions.
Web Site Home Web Site: PREMIER Biosoft International

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

Ascalaph Quantum Windows
3D graphic interface for the Quantum Mechanics program PC GAMESS. Ascalaph Quantum provides the generation and editing of molecular models.
Web Site Home Web Site: Agile Molecule

Beacon Designer Free Edition Internet Browser
Beacon Designer Free Edition is a free web based oligo properties calculator for analysing SYBR Green Primers and TaqMan Probes for possible secoondary structures such and for accurately calculating Primer and Probe Tm. Beacon Designer free edition also displays sequence details such as sequence length, runs, repeats, reverse, reverse complement and GC%.
Web Site Home Web Site: Premier Biosoft

BibioSphere PathwayEdition Internet Browser  Linux  Mac  Unix  Windows
BiblioSpherePE allows for dynamic data-driven network/pathway construction and analysis based on literature, the Genomatix Knowledge Base, and promoter DNA sequence analysis. It is an important component of the micro array data analysis pipeline offered by Genomatix.
Web Site Home Web Site: Genomatix

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

BioToolKit Mac  Windows
BioToolKit is a collection of tools frequently used by bench biomedical scientists. Functions include centrifugation speed/force conversion, molecular weight calculation for chemicals, oligos, and peptides, molar concentration calculator, OD calculator, recipe calculator, clinical calculator, primer design, peptide antigen design, grade book, and label printing.
Web Site Home Web Site: Chang Bioscience

Biochem 1.75 Windows
Biochem is an electronic biochemistry tutorial. Updates and expansions will make this multimedia document more comprehensive. Intended users are students and educators in settings ranging from high school to college. Requires Adobe Acrobat.
Download  (1063 kb, 29-Jun-1998)

Biochemical Pathways Internet Browser
Biochemical Pathways is the online version of Boehringer Mannheim's Biochemical Pathways chart. Fully searchable by keyword.
Web Site Home Web Site: Expasy

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

CELL Suite Windows
Incellico's Cell Suite being offered as a modular portfolio of research and discovery tools that will individually, and as a whole, respond to the specific challenges faced by life sciences researchers across the spectrum of biotechnology and bioinformatics problem solving. CELL acts as a librarian of public and private databases, automatically cross-referencing entities like genes and proteins that appear in those databases, and building a searchable, ontology-based network of cross-references that reveals the relationships between entities of interest to a user.
Web Site Home Web Site: Incellico

CLC Bioinformatics Cell Linux  Mac  Windows
CLC Bioinformatics Cell is a High Performance Computing product, accelerating Smith Waterman based BLAST-searches up to 400 times and Clustal W alignments up to 20 times. It can be run command line with the same parameters as NCBI BLAST, or through the graphical user interface of CLC Gene Workbench, CLC Protein Workbench, or CLC Combined Workbench.
Web Site Home Web Site: CLC Bioinformatics Cell

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 Free Workbench 1.0 Linux  Mac  Windows
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some bioinformatics features are: - GenBank searching and viewing (linear and circular views) - Multiple alignment of DNA, RNA and proteins (2 alignment algorithms) - Open reading frame determination - Translation from DNA to proteins (all genetic translation tables) - Reports with residue composition, molecular weight and iso electric point (for proteins) - Neighbor-joining and UPGMA phylogenies - Restriction site analysis and viewing - Other reporting facilities - Import/export to a number of data formats - Launch of external files - Detailed History Log
Web Site Home Web Site: CLC bio

CLC Gene Workbench Linux  Mac  Windows
CLC Gene Workbench 1.0 provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - 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 - Searches on GenBank and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

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