Online Services Bioinformatics Biology

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).

• PathCase: Pathways Database System - An integrated software system for storing, managing, analyzing, and querying metabolic pathways at genetic, molecular, biochemical and organism levels.
  
• Splice Miner - Tool for querying Evidence Viewer Database (EVDB), a comprehensive, non-redundant collection of splice variant data for human genes.
  
• PubCrawler - An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
  
• Canadian Bioinformatics Help Desk - We provide bioinformatics support, services, servers, and software to Canadian researchers.
  
• ProteinLounge - Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.
  
• Transterm - Interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences.
  
• Mobyle - Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour.
  
• Bioverse - Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.
  
• Carnac - A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
  
• Scansite - Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.
  
• 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, cont
  
• Ligand-Gated Ion Channel Database - LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
  
• 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.
  
• Center Structural Biology: Programs and Tools - User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.
  
• WebACT - 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 o
  
• 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.
  
• Biomolecular Interaction Network Database (BIND) - BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.
  
• Functional Human Gene Network - Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design.
  
• 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.
  
• Entrez Browser - Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
  
• LongTrace DNA Sequencing Service - A commercial service for improving the read length and quality of ABI 3730, 3130 and 3100 DNA sequencing traces. Works via reprocessing of the raw peak data before re-base calling. A free trial is provided.
  
• QGRS Mapper - Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes.
  
• BioGRID - Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.
  
• BiNCO-wiki - Provides a collection of information on data sources for biological networks, file formats that save biological networks and software to analyze the information of these sources.
  
• PEDANT - Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes
  
• ReadSeq - Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
  
• PIR-International Protein Sequence Database - Produces a non-redundant annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.
  
• Searching GenBank - Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).
  
• UEA Plant sRNA Toolkit - A suite of tools for the analysis of sRNA datasets from high-throughput sequencing experiments.
  
• Simulation Programs for Teaching Population Dynamics - Offers a number of educational programs including LESLIE, LOGIST, CHAOS, CELLS, WITCOM, PRED and LEWONTIN.
  
• Silva: Comprehensive Ribosomal RNA Databases - The provided databases comprise SSU and LSU sequences of all three domains. Online search and alignment tools are available and the results can be exported in ARB and FASTA format.
  
• Advanced Genetics Wizard - Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
  
• Mulan - 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.
  
• iHOP - Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
  
• Genepop on the Web - Online version of the program for populational genetics.
  
• TFM Explorer - Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.
  
• ProPred-I - An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.
  
• JustBio: Online Tool Set - A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.
  
• DBD: Transcription Factor Prediction Database - DBD is a database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families.
  
• IBM Bioinformatics Group - Tools & Content - Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.
  
• Bacterial Identification - Service for the identification of bacteria and fungi sequences by sequence alignment.
  
• Your Lab Data - A free web-based Laboratory Information Management System (LIMS), aimed at a typical small molecular biology laboratory allowing members to have their own private forum, events, Electronic Lab Notebook (ELN) and a LIMS area.
  
• PlasMapper - Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format.
  
• NIH BioInformatics and Molecular Analysis Section - Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the
  
• Gene and Protein Synonyms DataBase - Free service for retrieving all synonyms for a given gene or protein name.
  
• ERGO - Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a pattern-based analysis of genes and genomes.
  
• Gene Expression Data Analysis - Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation.
  
• Geneva Bioinformatics (GeneBio) S.A. - GeneBio provides proteomics software tools and databases including SWISS-PROT, PROSITE, SWISS-2DPAGE and Melanie. We also offer a secure version of ExPASy molecular biology web server.
  
• Center for Biological Sequence Analysis - Offers more than 30 online services for DNA and protein bioinformatics analysis.
  
• GenePattern - 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.
  
• Molecular Interactions Database (MINT) - MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA).
  
• My Genomics Resource Centre - A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.
  
• InstaSeq - Google-based search engine for DNA, RNA or Protein sequences.
  
• gp2fasta - 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.
  
• Zinc Finger Tools - Helps users design zinc finger transcription factors.
  
• YMF - DNA Motif Finding Program - Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.
  
• CUBIC: Columbia University Bioinformatics Center - Features PredictProtein service for sequence analysis and protein structure prediction, META for single-page interface to validated sequence analysis, PredictNLS for prediction and analysis of nuclear localization signals, EVA for evaluation of automatic
  
• 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,
  
• PANDORA - Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
  
• ParAlign - Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman.
  
• QualTrace DNA Sequencing - A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 and 3730xl traces files.
  
• BIOBASE - 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 regulato
  
• 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.
  
• Splice Center - Suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques.
  
• Information Génomique et Structurale (CNRS) - Online services including T-Coffee, El-Nemo, Casper and FeeBack.
  
• Systems Biology of Photosynthesis - Open web platform for modeling and reverse engineering of photosynthetic dynamism.
  
• Docking Server - Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.
  
• Sequence Analysis (Bielefeld University Bioinformatics Server) - Collection of sequence analysis tools.
  
• SA National Bioinformatics Institute - SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Resea
  
  

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