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

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T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. / Smith, Cindy; Danilowicz, Bret; Clear, Adrian et al.
In: FEMS Microbiology Ecology, Vol. 54, No. 3, 05.2005, p. 375-380.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

Smith, C, Danilowicz, B, Clear, A, Costello, F, Wilson, B & Meijer, W 2005, 'T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles', FEMS Microbiology Ecology, vol. 54, no. 3, pp. 375-380. https://doi.org/10.1016/j.femsec.2005.05.002

APA

Smith, C., Danilowicz, B., Clear, A., Costello, F., Wilson, B., & Meijer, W. (2005). T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiology Ecology, 54(3), 375-380. https://doi.org/10.1016/j.femsec.2005.05.002

Vancouver

Smith C, Danilowicz B, Clear A, Costello F, Wilson B, Meijer W. T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiology Ecology. 2005 May;54(3):375-380. doi: 10.1016/j.femsec.2005.05.002

Author

Smith, Cindy ; Danilowicz, Bret ; Clear, Adrian et al. / T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. In: FEMS Microbiology Ecology. 2005 ; Vol. 54, No. 3. pp. 375-380.

Bibtex

@article{2046562ede4d45229f14de3f825a6a29,
title = "T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles",
abstract = "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-basedprogram, 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 comparisonof 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 TAlign.",
keywords = "tRFLP, Computer algorithm, Community analysis",
author = "Cindy Smith and Bret Danilowicz and Adrian Clear and Fintan Costello and Bryan Wilson and Wim Meijer",
year = "2005",
month = may,
doi = "10.1016/j.femsec.2005.05.002",
language = "English",
volume = "54",
pages = "375--380",
journal = "FEMS Microbiology Ecology",
issn = "0168-6496",
publisher = "Wiley-Blackwell",
number = "3",

}

RIS

TY - JOUR

T1 - T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles

AU - Smith, Cindy

AU - Danilowicz, Bret

AU - Clear, Adrian

AU - Costello, Fintan

AU - Wilson, Bryan

AU - Meijer, Wim

PY - 2005/5

Y1 - 2005/5

N2 - 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-basedprogram, 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 comparisonof 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 TAlign.

AB - 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-basedprogram, 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 comparisonof 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 TAlign.

KW - tRFLP

KW - Computer algorithm

KW - Community analysis

U2 - 10.1016/j.femsec.2005.05.002

DO - 10.1016/j.femsec.2005.05.002

M3 - Journal article

VL - 54

SP - 375

EP - 380

JO - FEMS Microbiology Ecology

JF - FEMS Microbiology Ecology

SN - 0168-6496

IS - 3

ER -