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
Literature & Tutorials:
This record last updated: 10-02-2007