Characterizing patterns in DNA sequence trace data through informatics tools

Detalhes bibliográficos
Autor(a) principal: Mendonça, Pedro Alberto Fernández de
Data de Publicação: 2008
Tipo de documento: Dissertação
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10316/28656
Resumo: Dissertação de mestrado em Biologia Celular e Molecular, apresentada ao Departamento de Zoologia da Faculdade de Ciências e Tecnologia da Universidade de Coimbra.
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spelling Characterizing patterns in DNA sequence trace data through informatics toolsSequence trace dataPeak height patternsSequence BiometricsExpert SystemsDissertação de mestrado em Biologia Celular e Molecular, apresentada ao Departamento de Zoologia da Faculdade de Ciências e Tecnologia da Universidade de Coimbra.Sequence trace data files produced by the Sanger sequencing method were believed to create peak height values of random height and with no added value for base calling. Our study is the first to comprehensively prove the existence of definable peak height patterns and to develop tools that allow the characterization of the frequency of such patterns for each sequence frame. By studying hundreds of mtDNA samples sequenced in two certified forensic laboratories, in the United States of America and in Portugal, we were able to prove that peak height patterns are predictable and the same from sample to sample if the chemistry and primer combination is kept constant within the same laboratory. Moreover, the characterization of these patterns and the ability to predict their behavior for other samples led us to develop the novel concept of Sequence Biometrics. Sequence Biometrics defines the characteristics of these peak height patterns for a certain stretch of sequenced DNA, independently of the origin and sample, which is specific to the primer/chemistry combination used within the laboratory. Therefore, Sequence Biometrics is a new quality parameter for sample processing and can be used by novel expert systems in the assessment of new data. This work provides the basic informatics tools and workflow mechanisms to build standard Sequence Biometrics tables, of several primer/chemistry combinations and to define their characteristics and boundaries of its use.2008info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesishttp://hdl.handle.net/10316/28656http://hdl.handle.net/10316/28656engMendonça, Pedro Alberto Fernández deinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-01-20T17:49:44Zoai:estudogeral.uc.pt:10316/28656Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:57:06.293777Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Characterizing patterns in DNA sequence trace data through informatics tools
title Characterizing patterns in DNA sequence trace data through informatics tools
spellingShingle Characterizing patterns in DNA sequence trace data through informatics tools
Mendonça, Pedro Alberto Fernández de
Sequence trace data
Peak height patterns
Sequence Biometrics
Expert Systems
title_short Characterizing patterns in DNA sequence trace data through informatics tools
title_full Characterizing patterns in DNA sequence trace data through informatics tools
title_fullStr Characterizing patterns in DNA sequence trace data through informatics tools
title_full_unstemmed Characterizing patterns in DNA sequence trace data through informatics tools
title_sort Characterizing patterns in DNA sequence trace data through informatics tools
author Mendonça, Pedro Alberto Fernández de
author_facet Mendonça, Pedro Alberto Fernández de
author_role author
dc.contributor.author.fl_str_mv Mendonça, Pedro Alberto Fernández de
dc.subject.por.fl_str_mv Sequence trace data
Peak height patterns
Sequence Biometrics
Expert Systems
topic Sequence trace data
Peak height patterns
Sequence Biometrics
Expert Systems
description Dissertação de mestrado em Biologia Celular e Molecular, apresentada ao Departamento de Zoologia da Faculdade de Ciências e Tecnologia da Universidade de Coimbra.
publishDate 2008
dc.date.none.fl_str_mv 2008
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10316/28656
http://hdl.handle.net/10316/28656
url http://hdl.handle.net/10316/28656
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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