Spoligologos: a bioinformatic approach to displaying and analyzing Mycobacterium tuberculosis data

Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gai...

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Published inEmerging infectious diseases Vol. 8; no. 11; pp. 1306 - 1309
Main Authors Driscoll, Jeffrey R, Bifani, Pablo J, Mathema, Barun, McGarry, Michael A, Zickas, Genét M, Kreiswirth, Barry N, Taber, Harry W
Format Journal Article
LanguageEnglish
Published United States U.S. National Center for Infectious Diseases 01.11.2002
Centers for Disease Control and Prevention
Subjects
Bacterial Typing Techniques
bioinformatics
Computational Biology - methods
Databases, Factual
Dispatch
DNA Fingerprinting
DNA testing
DNA, Bacterial - analysis
DNA, Bacterial - genetics
DNA, Intergenic - analysis
Evaluation
Genotype
Humans
Mycobacteria
Mycobacterium tuberculosis - genetics
Oligonucleotides - genetics
Polymerase chain reaction
spoligotyping
Tuberculosis
United States
United States
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Abstract Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. Logo analysis of spoligotyping data provides a simple way to describe a fingerprint signature and may be useful in categorizing unique spoligotypes patterns as they are discovered. Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. The description of related spoligotypes has depended on exhaustive listings of the individual spoligotyping patterns. Logo analysis may become another useful graphic method of visualizing and presenting spoligotyping clusters from these databases.
AbstractList Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. Logo analysis of spoligotyping data provides a simple way to describe a fingerprint signature and may be useful in categorizing unique spoligotypes patterns as they are discovered. Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. The description of related spoligotypes has depended on exhaustive listings of the individual spoligotyping patterns. Logo analysis may become another useful graphic method of visualizing and presenting spoligotyping clusters from these databases.
Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction–based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. Logo analysis of spoligotyping data provides a simple way to describe a fingerprint signature and may be useful in categorizing unique spoligotypes patterns as they are discovered. Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. The description of related spoligotypes has depended on exhaustive listings of the individual spoligotyping patterns. Logo analysis may become another useful graphic method of visualizing and presenting spoligotyping clusters from these databases.
Audience Professional
Academic
Author Driscoll, Jeffrey R
Kreiswirth, Barry N
Taber, Harry W
Bifani, Pablo J
Mathema, Barun
McGarry, Michael A
Zickas, Genét M
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Snippet Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex....
Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction–based method of DNA fingerprinting the Mycobacterium tuberculosis complex....
Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction–based method of DNA fingerprinting the Mycobacterium tuberculosis complex....
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StartPage 1306
SubjectTerms Bacterial Typing Techniques
bioinformatics
Computational Biology - methods
Databases, Factual
Dispatch
DNA Fingerprinting
DNA testing
DNA, Bacterial - analysis
DNA, Bacterial - genetics
DNA, Intergenic - analysis
Evaluation
Genotype
Humans
Mycobacteria
Mycobacterium tuberculosis - genetics
Oligonucleotides - genetics
Polymerase chain reaction
spoligotyping
Tuberculosis
United States
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Title Spoligologos: a bioinformatic approach to displaying and analyzing Mycobacterium tuberculosis data
URI https://www.ncbi.nlm.nih.gov/pubmed/12453361
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https://search.proquest.com/docview/72722082
https://pubmed.ncbi.nlm.nih.gov/PMC2738554
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