Directory of Online Services Resources

Home > Science > Biology > Bioinformatics > Online Services

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).

Subcategories

• Directories
• Ecological Databases
• Gene Expression and Regulation
• Genome Databases
• Homology Detection
• Molecular Biology Tools
• Phylogenetic Analysis
• Protein Analysis

Resources in This Category

• Advanced Genetics Wizard

  http://www.geneticswizard.com/
  Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.

• BIOBASE

  http://www.gene-regulation.com/
  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.

• BioGRID

  http://www.thebiogrid.org/
  Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.

• BioModels Database

  http://www.ebi.ac.uk/biomodels/
  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

  http://www.bu.edu/bmerc/
  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.

• Carnac

  http://bioinfo.lifl.fr/carnac/
  A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.

• Center for Biological Sequence Analysis

  http://www.cbs.dtu.dk/services/
  Offers more than 30 online services for DNA and protein bioinformatics analysis.

• Center Structural Biology: Programs and Tools

  http://www.csb.yale.edu/
  User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.

• Docking Server

  http://www.dockingserver.com/
  Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.

• Gene2MeSH

  http://gene2mesh.ncibi.org/
  Web application that searches gene symbols or MeSH terms and displays resulting pairs of genes and MeSH terms that match the search term.

• GenePattern

  http://www.genepattern.org/
  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

  http://genepop.curtin.edu.au/
  Online version of the program for populational genetics.

• Geneva Bioinformatics (GeneBio) S.A.

  http://www.genebio.com/
  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

  http://genouest.org/
  Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news.

• gp2fasta

  http://gp2fasta.ovh.org/
  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.

• iHOP

  http://www.ihop-net.org/UniPub/iHOP/
  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

  http://acer.gen.tcd.ie/
  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

  http://www.justbio.com/
  A suite of online tools for analysis of DNA/RNA, proteins and arrays.

• Ligand-Gated Ion Channel Database

  http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
  LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.

• Malaysian Genomics Resource Centre Berhad

  http://www.mgrc.com.my/
  MGRC provides contract genomes services, sequencing services, data and access services.

• Metab2MeSH

  http://metab2mesh.ncibi.org/
  Web application that searches biological substances or MeSH terms and displays resulting pairs of substances and MeSH terms that match the search term.

• Mobyle

  http://mobyle.pasteur.fr/
  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

  http://www.ifti.org/
  Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.

• Mulan

  http://mulan.dcode.org/
  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.

• PANDORA

  http://www.pandora.cs.huji.ac.il/
  Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.

• PubCrawler

  http://pubcrawler.gen.tcd.ie/
  An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.

• Systems Biology of Photosynthesis

  http://www.e-photosynthesis.org/
  Open web platform for modeling and reverse engineering of photosynthetic dynamism.

• TFM Explorer

  http://bioinfo.lifl.fr/TFM/TFME/
  Scans sequences for potential transcription factor binding sites using JASPAR and TRANSFAC.

• Transcription Element Search Software (TESS)

  http://www.cbil.upenn.edu/cgi-bin/tess/tess
  Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.

• Verbumculus Genetic Sequence Analyzer

  http://www.cs.ucr.edu/~stelo/Verbumculus/
  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.

• WebACT

  http://www.webact.org/
  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.

• Zinc Finger Tools

  http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
  Helps users design zinc finger transcription factors.

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