Characterizing patterns in DNA sequence trace data through informatics tools
Autor(a) principal: | |
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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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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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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 |
|
_version_ |
1799133859429744640 |