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).
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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.
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.
Advanced Genetics Wizard
Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
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.
Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.
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.
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.
Biomolecular Interaction Network Database (BIND)
BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.
Broad Institute: Software
Scientists at the Broad Institute have developed a range of software tools for the analysis of increasingly large genome-related datasets. These are openly available to the scientific community.
A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
Center for Biological Sequence Analysis
Offers more than 30 online services for DNA and protein bioinformatics analysis.
Center Structural Biology: Programs and Tools
User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.
Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.
Web application that searches gene symbols or MeSH terms and displays resulting pairs of genes and MeSH terms that match the search term.
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.
Genepop on the Web
Online version of the program for populational genetics.
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.
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.
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.
Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
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
JustBio: Online Tool Set
A suite of online tools for analysis of DNA/RNA, proteins and arrays.
Ligand-Gated Ion Channel Database
LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
Malaysian Genomics Resource Centre Berhad
MGRC provides contract genomes services, sequencing services, data and access services.
Web application that searches biological substances or MeSH terms and displays resulting pairs of substances and MeSH terms that match the search term.
Michigan Molecular Interactions
MiMi Web provides an interface to a NCIBI data repository for conducting systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research sources.
Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour.
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.
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.
Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
Systems Biology of Photosynthesis
Open web platform for modeling and reverse engineering of photosynthetic dynamism.
Scans sequences for potential transcription factor binding sites using JASPAR and TRANSFAC.
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.
YMF - DNA Motif Finding Program
Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.
Zinc Finger Tools
Helps users design zinc finger transcription factors.
Last update:July 20, 2016 at 12:05:04 UTC