Selection of enzymes for terminal restriction fragment length polymorphism analysis of fungal internally transcribed spacer sequences.

ABSTRACT: Terminal restriction fragment length polymorphism (TRFLP) profiling of the internally transcribed spacer (ITS) ribosomal DNA of unknown fungal communities is currently unsupported by a broad-range enzyme-choosing rationale. An in silico study of terminal fragment size distribution was therefore performed following virtual digestion (by use of a set of commercially available 135 type IIP restriction endonucleases) of all published fungal ITS sequences putatively annealing to primers ITS1 and ITS4. Different diversity measurements were used to rank primer-enzyme pairs according to the richness and evenness that they showed. Top-performing pairs were hierarchically clustered to test for data dependency. The enzyme set composed of MaeII, BfaI, and BstNI returned much better results than random

SUBMITTER: Alvarado P 

PROVIDER: S-EPMC2708443 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature