REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis

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...

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Podrobná bibliografie
Vydáno v:	Nucleic acids research Ročník 35; číslo suppl-2; s. W58 - W62
Hlavní autoři:	Collins, Roy Eric, Rocap, Gabrielle
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford University Press 01.07.2007
Témata:	Algorithms Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Computational Biology - methods Databases, Factual DNA, Bacterial - analysis DNA, Bacterial - genetics DNA, Ribosomal - analysis DNA, Ribosomal - genetics Ecosystem Enzymes - chemistry Internet Microbiology Phylogeny Polymorphism, Restriction Fragment Length RNA, Ribosomal, 16S - genetics Software User-Computer Interface
ISSN:	0305-1048, 1362-4962, 1362-4962
On-line přístup:	Získat plný text
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Popis
Shrnutí:	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. The web server is available without access restrictions at http://rocaplab.ocean.washington.edu/tools/repk.
Bibliografie:	http://www.nar.oupjournals.org/ istex:77B86DF131371FBB32B00E6F7B993CD0249DFCEB ark:/67375/HXZ-SG5TNBLK-3 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gkm384