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Why feature free applications on UBI's website?  Like you, we prefer to only pay for items when necessary.  There are many free applications that can do tasks that molecular biologists require.  We can save you time by putting these here.  The reasons why people graduate from free to commercial applications that we market are:

  • Scale - Most of the free applications are fine with a few sequences, results, etc. but the work flow, storage requirements, administrative needs, become untenable in many cases after as few as 100 instances (sequences, results).
  • Support - Free applications do not provide extensive help or support resources.  At some point, your time becomes more valuable than what the free application is demanding.
  • User Interface - Often free applications do not have a sophisticated graphical user interface.  This makes it more difficult to learn and use them.  

Applications (Free)

  • BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. It is released under the GNU General Public License.
  • European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics.  To view all tools click here.
  • NetPrimer combines the latest primer design algorithms with a web-based interface allowing the user to analyze primers over the Internet.
  • TIGR The microarray software development team at TIGR (led by Dr. John Quackenbush) has been very busy producing a software suite entitled TM4.

Links

Title Description
Bioinformatics Links Directory The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.
BioSupplyNet Database of biotechnology vendors.
CBHD Newsletter Canadian Bioinformatics Help Desk is an excellent source for bioinformaticians whether in the public or private domain.
Codon Usage Tables Codon usage tabulated from GenBank.
EndNote and Reference Manager EndNote®, ProCite®, Reference Manager® are software tools for publishing and managing bibliographies on the Windows and Macintosh® desktop. 
Guide to Sequence Analysis This guide will introduce the reader to molecular sequence analysis.
Microarray Analysis Methods Here is a very interesting article from Modern Drug Discovery that reviews techniques used to analyze microarray data. The techniques range from unsupervised methods such as hierarchical clustering and self-organized maps (SOMs) to supervised methods such as the "nearest-neighbor" approach, classification trees, support vector machines (SVMs), and neural networks. Some of the supervised software packages that are currently available include: MIT's GeneCluster, Silicon Genetics' GeneSpring, and BioDiscovery's GeneSight.  Source: Modern Drug Discovery
National Center for Biotechnology Information Entrez, GenBank, homology searches and more.
ORF Finder  Find open reading frames from NCBI.
PA Subcellular Localization Web Server Believed to be the world's most accurate and comprehensive predictor of protein sub-cellular localization. 
PNA primer design guidelines Applied Biosystems guidelines for sequence design of PNA oligomers.
Rebase The Restriction Enzyme Database.
ScienceSlides ScienceSlides is a PowerPoint-dedicated software for speakers and educators in general biomedical fields.
STS Finder Find a sequence tagged site primer in your genomic sequence from NCBI.
 
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Last modified: April 08, 2012