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Free Online Bioinformatics Tools

PapersIn recognition of a fresh new year and a fresh new direction for Bitesize Bio, I thought I’d start my tenure as the fresh new Bioinformatics “guru” by introducing you to a handful of websites that will help you locate established as well as fresh new and (mostly) free online molecular biology and bioinformatics databases and tools.

And I promise not to use the phrase “fresh new” again.

There are already thousands of online bioinformatics resources available, with undoubtedly many more to come. One of the limiting factors of the field is the difficulty in navigating the vast array of resources to identify the most appropriate tool(s) for what you need to do, whether that’s finding information on SNPs, locating pathway analysis software, or designing PCR primers. Here are four websites that will help you with your search.

 

The OBRC contains links and annotations for over 2,000 bioinformatics databases and software tools. It was created in 2006 by the Molecular Biology Information Service for the Health Sciences Library System at the University of Pittsburgh and can be accessed from their webpage via search.HSLS.MolBio. The purpose of the manually curated OBRC is to bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources. This freely available, searchable database arranges resources by categories and sub-categories such as Structure Databases and Analysis Tools, Proteomics Resources, and Enzymes and Pathways. The OBRC is the largest online collection of its kind and the only one with advanced search results clustering. It is a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. Full disclosure: although I didn’t create the OBRC, I am currently its curator. Feel free to contact me if you have any questions or suggestions.

BioMed Central Databases

The BioMed Central Databases maintains a catalog of Web-based databases as well as a Biology Image Library. The collection can be browsed by subject area or searched by name, description, contents, and/or subject area. The scientific community is welcome to create a database or simply house it on the BioMed Central Databases site.

OReFiL

OReFiL is the Online Resource Finder for Lifesciences. Developed by computational biologists, it provides searches for online resources introduced in peer-reviewed papers in the life sciences. A crawler automatically extracts all URLs listed in MEDLINE abstracts and full-text papers from BioMed Central open-access journals and maintains them in a freely available, searchable database.

Nucleic Acids Research Bioinformatics Links Directory

The Bioinformatics Links Directory features curated links to molecular resources, tools, and databases culled from the annual Database issue and Web Server issue of the journal Nucleic Acids Research (NAR). NAR is a highly ranked open access journal that publishes articles on the biological, biochemical, physical, and chemical aspects of proteins and nucleic acids involved in nucleic acid interactions and/or metabolism. The freely available Bioinformatics Link Directory provides links to the resources themselves, as well as to the NAR published articles about those resources.

Happy hunting! And please leave comments, especially if you know of other meta-resources for bioinformatics tools and databases.

7 Comments

  1. Jose Luis Marina on October 14, 2010 at 8:04 pm

    If anyone is interested on biomedical text mining and extracting normalized concepts from text give BioLabeler a try:
    http://www.biolabeler.com

  2. nelson adams on September 8, 2010 at 10:09 pm

    really i got very much information about Online Bioinformatics Resource Collection
    thank you kepp doing it.
    *********
    nelson
    Tool Insurance

  3. nelson adams on September 8, 2010 at 10:09 pm

    really i got very much information about Online Bioinformatics Resource Collection
    thank you kepp doing it.
    *********
    nelson
    Tool Insurance

  4. Manu on March 1, 2010 at 10:18 am

    When I need simple basic tools for DNA manipulation, or to create random DNA and proteins, I usually use the online bioinformatics tools at http://www.bioinfx.co.cc

  5. Evelyn on December 8, 2009 at 10:04 pm

    http://www.bioinfoman.com requires registration, but is free for individual users.

    They have multiple programs that I find useful for my lab–BxItems is the best–I don’t think we’ll ever lose a sample or reagent again! We also use BxSeqTools for all of our sequencing work. The system is fully integrated with BLAST and works great for creating foolproof constructs.

    There is a demo link you can check out on the homepage so you can see what I’m talking about without having to register 🙂

  6. LParnell on January 15, 2009 at 5:41 pm

    A nice collection of basic tools that I have often used and recommended to my students can be found at http://www.bioinformatics.org. This group is based out of the University of Massachusetts at Lowell.

  7. Al Shapiro on January 14, 2009 at 9:35 pm

    Hi!

    Another great Free/No registration required on-line BioInformatics Resource…

    The “G6G Directory of Omics and Intelligent Software” “www.g6g-softwaredirectory.com” published by G6G Consulting Group. This directory lists data mining and additional software that is from two exciting and increasingly integrated technology fields, those of biotechnology and artificial intelligence.

    Currently contains over 280 different advanced Software product abstracts (Not just links)… and it is searchable via Google…

    In the Software Products by Application, products are listed in two sections.

    (1) Omics and Intelligent Software for Biological Scientists,
    Biostatisticians, Bio-IT Students & Professionals, Life Science
    Researchers, Students and Mathematical Biologists.

    Each product is categorized by a major biotechnology group followed by subgroups:

    Genomics

    Gene Expression Analysis/Profiling/Tools
    Gene Expression Database/Tools
    Genetic Data Analysis/Tools
    Research Project Design/Tools

    Cross-omics

    Biomarker Discovery/Analysis/Tools
    Data/Text Mining Systems/Tools
    Knowledge Bases/Databases/Tools
    Next Generation Sequence Analysis/Tools
    Pathway Analysis/Tools
    Pathway Knowledge Bases/Databases/Tools
    Sequence Analysis/Tools

    Proteomics

    Mass Spectrometry Analysis/Tools

    (2) Intelligent Software for Software Developers, Bio-IT Students
    & Professionals, and IT Students & Professionals

    Each product is categorized by a major “Intelligent” technology group:

    Intelligent Software

    Bayesian Network Systems/Tools
    Data Mining Systems/Tools
    Expert (Knowledge Based) Systems/Tools
    Fuzzy Logic Systems/Tools
    Gene Expression Programming Systems/Tools
    Genetic Algorithm Systems/Tools
    Genetic Programming Systems/Tools
    Neural Network Systems/Tools

    Take a look…

    Al Shapiro

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