REPK -- An analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis

What you can do:
Maximize your ability to discriminate terminal restriction fragments obtained during T-RFLP to take advantage of this powerful community fingerprinting technique.
Highlights:
  • Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widespread technique for rapidly fingerprinting microbial communities.
  • Users of T-RFLP frequently overlook the resolving power of well-chosen restriction endonucleases and often fail to report how they chose their enzymes.
  • REPK (Restriction Endonuclease Picker) assists in the rational choice of restriction endonucleases for T-RFLP by finding sets of four restriction endonucleases that together uniquely differentiate user-designated sequence groups.
  • With REPK, users can provide their own sequences (of any gene, not just 16S rRNA), specify the taxonomic rank of interest and choose from a number of filtering options to further narrow down the enzyme selection.
  • Bug tracking is provided, and the source code is open and accessible under the GNU Public License v.2, at http://code.google.com/p/repk.
Keywords:
  • Algorithms
  • Bacteria/*classification/genetics/isolation & purification
  • Computational Biology/*methods
  • DNA, Bacterial/analysis/genetics
  • DNA, Ribosomal/analysis/genetics
  • Enzymes/chemistry
  • Microbiology
  • Phylogeny
  • Polymorphism, Restriction Fragment Length
  • RNA, Ribosomal, 16S/*genetics
  • User-Computer Interface
This record last updated: 10-02-2007
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