T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles

Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time c...

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Vydané v:FEMS microbiology ecology Ročník 54; číslo 3; s. 375 - 380
Hlavní autori: Smith, Cindy J., Danilowicz, Bret S., Clear, Adrian K., Costello, Fintan J., Wilson, Bryan, Meijer, Wim G.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Oxford, UK Elsevier B.V 01.11.2005
Blackwell Publishing Ltd
Blackwell
Oxford University Press
Predmet:
Alignment
Bacteria - genetics
Bacterioplankton
Biological and medical sciences
Communities
Community analysis
Comparative analysis
Computer algorithm
DNA Primers
Ecology
Ecosystem
Fluorescence
Fundamental and applied biological sciences. Psychology
Genetic Techniques
Internet
Microbial activity
Microbiology
Microorganisms
Plankton - genetics
Polymorphism
Polymorphism, Restriction Fragment Length
Restriction fragment length polymorphism
Software
Species Specificity
tRFLP
North Atlantic
Celtic Sea
Irish Sea
Atlantic Ocean
tRFLP
Computer algorithm
Community analysis
High throughput screening
Restriction fragment length polymorphism
Microbiology
Genotype
Ecology
Identification
Method
Microbial community
ISSN:0168-6496, 1574-6941
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Popis
Shrnutí:Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align ( http://inismor.ucd.ie/~talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Align.
Bibliografia:Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester C04 3SQ, United Kingdom.
Allen E. Paulson College of Science and Technology, Georgia Southern University, P.O. Box 8044, Statesboro, GA 30460, USA.
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ISSN:0168-6496
1574-6941
DOI:10.1016/j.femsec.2005.05.002