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Doctoral Thesis
DOI
10.11606/T.95.2009.tde-17092010-123112
Document
Author
Full name
Mauricio Egidio Cantão
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 2009
Supervisor
Committee
Ferreira, João Eduardo (President)
Carrer, Helaine
Ciferri, Ricardo Rodrigues
Ruiz, Duncan Dubugras Alcoba
Vasconcelos, Ana Tereza Ribeiro de
Title in Portuguese
Abordagem algébrica para seleção de clones ótimos em projetos genomas e metagenomas
Keywords in Portuguese
Álgebra de Processos
Clones Ótimos
Metagenoma
Microarranjo de DNA
NPDL
Workflow Cintífico
Abstract in Portuguese
Devido à grande diversidade de microrganismos desconhecidos no meio ambiente, 99% deles não podem ser cultivados nos meios de cultura tradicionais dos laboratórios. Para isso, projetos metagenômicos são propostos para estudar comunidades microbianas presentes no meio ambiente, a partir de técnicas moleculares, em especial o seqüenciamento. Dessa forma, para os próximos anos é esperado um acúmulo de seqüências produzidas por esses projetos. As seqüências produzidas pelos projetos genomas e metagenomas apresentam vários desafios para o tratamento, armazenamento e análise, como exemplo: a busca de clones contendo genes de interesse. Este trabalho apresenta uma abordagem algébrica que define e gerencia de forma dinâmica as regras para a seleção de clones em bibliotecas genômicas e metagenômicas, que se baseiam em álgebra de processos. Além disso, uma interface web foi desenvolvida para permitir que os pesquisadores criem e executem facilmente suas próprias regras de seleção de clones em bancos de dados de seqüências genômicas e metagenômicas. Este software foi testado em bibliotecas genômicas e metagenômicas e foi capaz de selecionar clones contendo genes de interesse.
Title in English
Algebraic approach to optimal clone selection in genomics and metagenomics projects.
Keywords in English
DNA Microarray
Metagenome
NPDL
Optimal Clones
Process Algebra
Scientific Workflow
Abstract in English
Due to the wide diversity of unknown organisms in the environment, 99% of them cannot be grown in traditional culture medium in laboratories. Therefore, metagenomics projects are proposed to study microbial communities present in the environment, from molecular techniques, especially the sequencing. Thereby, for the coming years it is expected an accumulation of sequences produced by these projects. Thus, the sequences produced by genomics and metagenomics projects present several challenges for the treatment, storing and analysis such as: the search for clones containing genes of interest. This work presents an algebraic approach that defines it dynamically and manages the rules of the selection of clones in genomic and metagenomic libraries, which are based on process algebra. Furthermore, a web interface was developed to allow researchers to easily create and execute their own rules to select clones in genomic and metagenomic sequence database. This software was tested in genomics and metagenomics libraries and it was able to select clones containing genes of interest.
 
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Mauricio_Cantao.pdf (1.17 Mbytes)
Publishing Date
2011-01-05
 
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