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With the explosion in the amount of DNA and protein sequence available, many organizations offer web-based access to programs which process this information in some way. This category entails the many different services that are open for use by private or public organizations for the purpose of biological computation or services (i.e. informative bioinformatics databases).- Category ID : 417107
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GenOuest Bioinformatics Platform

Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news.
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Center Structural Biology: Programs and Tools

User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.
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Geneva Bioinformatics (GeneBio) S.A.

Provides proteomics software tools and databases including SWISS-PROT, PROSITE, SWISS-2DPAGE and Melanie. They also offer a secure version of ExPASy molecular biology web server.
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INCBI Irish National Centre for BioInformatics

Hosts Irish embnet node, Gives links to Database browsing and interrogation at SRS, European (EBI) servers, Blast server for parasite genomes (EBI), US (NCBI) servers, Protein structure prediction, PredictProtein Server in Heidelberg, Gene identification, splice sites, exons, introns and a list of gene structure prediction programs
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Molecular Informatics Resource for the Analysis of Gene Expression

Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.
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Verbumculus Genetic Sequence Analyzer

An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program.
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The focus of the GBF project "Molecular Bioinformatics of Gene Regulation" are regulatory genomic signals and regions that govern transcriptional control based on TRANSFAC - The Transcription Factor Database. It compiles data about gene regulatory DNA sequences and protein factors binding to and acting through them.
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Performs single-coverage local multiple DNA sequence alignments of finished and draft-quality genome sequences. It also provides with an option to predict transcription factor binding sites evolutionarily conserved across multiple species.
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Systems Biology of Photosynthesis

Open web platform for modeling and reverse engineering of photosynthetic dynamism.
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A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
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An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
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Advanced Genetics Wizard

Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
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Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
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A database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool. User can perform their comparisons on their own data.
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BioModels Database

Resource for storing, searching and retrieving published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
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Center for Biological Sequence Analysis

Offers more than 30 online services for DNA and protein bioinformatics analysis.
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Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
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Malaysian Genomics Resource Centre Berhad

MGRC provides contract genomes services, sequencing services, data and access services.
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Ligand-Gated Ion Channel Database

LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
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Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.
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Zinc Finger Tools

Helps users design zinc finger transcription factors.
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Transcription Element Search Software (TESS)

Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.
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Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour.
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Docking Server

Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.
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This platform provides over 100 methods for the analysis and visualization of gene expression, copy number, proteomic and other data. It enables biologists to add new analyses and create workflows that can be shared, edited and published.
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Converts gp files from NCBI GenPept format to fasta. Its main purpose is to create fasta files with short, but still accurate headers for sequence.
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Web application that searches gene symbols or MeSH terms and displays resulting pairs of genes and MeSH terms that match the search term.
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Web application that searches biological substances or MeSH terms and displays resulting pairs of substances and MeSH terms that match the search term.
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TFM Explorer

Scans sequences for potential transcription factor binding sites using JASPAR and TRANSFAC.
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JustBio: Online Tool Set

A suite of online tools for analysis of DNA/RNA, proteins and arrays.
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Genepop on the Web

Online version of the program for populational genetics.
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BioMolecular Engineering Research Center

Tools and methods for computational biology. Working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through bioinformatics.

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