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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| Published in: | FEMS microbiology ecology Vol. 54; no. 3; pp. 375 - 380 |
|---|---|
| Main Authors: | , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Oxford, UK
Elsevier B.V
01.11.2005
Blackwell Publishing Ltd Blackwell Oxford University Press |
| Subjects: | |
| ISSN: | 0168-6496, 1574-6941 |
| Online Access: | Get full text |
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| 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-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. |
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| AbstractList | 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. 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. 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-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. 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.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. |
| Author | Danilowicz, Bret S. Smith, Cindy J. Clear, Adrian K. Costello, Fintan J. Wilson, Bryan Meijer, Wim G. |
| Author_xml | – sequence: 1 givenname: Cindy J. surname: Smith fullname: Smith, Cindy J. organization: Department of Zoology, University College Dublin, Dublin 4, Ireland – sequence: 2 givenname: Bret S. surname: Danilowicz fullname: Danilowicz, Bret S. organization: Department of Zoology, University College Dublin, Dublin 4, Ireland – sequence: 3 givenname: Adrian K. surname: Clear fullname: Clear, Adrian K. organization: Department of Computer Science, University College Dublin, Dublin 4, Ireland – sequence: 4 givenname: Fintan J. surname: Costello fullname: Costello, Fintan J. organization: Department of Computer Science, University College Dublin, Dublin 4, Ireland – sequence: 5 givenname: Bryan surname: Wilson fullname: Wilson, Bryan organization: Department of Industrial Microbiology, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland – sequence: 6 givenname: Wim G. surname: Meijer fullname: Meijer, Wim G. email: wim.meijer@ucd.ie organization: Department of Industrial Microbiology, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17238073$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/16332335$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | 2005 Federation of European Microbiological Societies 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. 2005 2005 INIST-CNRS 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. |
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| Issue | 3 |
| Keywords | tRFLP Computer algorithm Community analysis High throughput screening Restriction fragment length polymorphism Microbiology Genotype Ecology Identification Method Microbial community |
| Language | English |
| License | CC BY 4.0 |
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| Notes | 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. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Feature-1 content type line 23 |
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| PublicationDate | November 2005 |
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| Snippet | Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison... Abstract Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities.... Terminal restriction fragment length polymorphism (tRFLP) is a potentially high‐throughput method for the analysis of complex microbial communities. Comparison... |
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| SubjectTerms | 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 |
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| Title | T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles |
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