Implementation of a plant-associated bacteria proteome database:ProBacter / Implementação de um banco de dados de proteomas de bactérias associadas a plantas: ProBacter

AUTOR(ES)

Fernanda Nascimento Almeida

DATA DE PUBLICAÇÃO

2007

RESUMO

This dissertation offers a computation approach to comparative analysis between cmpletely sequenced genomes of plant-associated bacteria. The created system was denominated ProBacter and it is composed of a relational database and computational tools for sequence analysis. The database was created from a diverse data source, including information from GenBank, TrEMBL, Interpro, COG and GO. The proteins were organized into clusters through the BBH (Bidirectional Best Hits) methodology and categorized according to the functional classification of the Xanthomonas Genome Project. Each entry displayed by the system in a friendly user interface corresponds to an information sheet with the gene and protein sequence, functional category, domain prediction, and related scientific publications, in addition to the group that it belongs, and external links. The system offers a search interface similar to other database systems with pre-formatted queries. For advanced queries, the user has access to an interface that can be used without previous knowledge of the SQL language or ProBacters database arquiteture. The BLASTP program and two multiple sequence alignment tools, namely ClustalW and T-Coffee, were integrated into the system as well, allowing internal and external sequence comparison. In addition, the system makes available visualization tools capable of displaying the gene position inside a genome and BHH links of clusters. Also, the user is capable of adding new information for each gene in the system. ProBacters goal is to collect information available from a large source of databases into one computational environment, organize this information and offer comparative tools for sequence analysis.

ASSUNTO(S)

genomics computabilidade e modelos de computacao proteomas computational biology genômica comparativa proteomics bioinformatics database probacter base de dados probacter biologia computacional bioinformática

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