Gene projects: a genome web tool for ongoing mining and annotation applied to CitEST

Carazzolle, Marcelo Falsarella; Formighieri, Eduardo Fernandes; Digiampietri, Luciano Antônio; Araújo, Marcos Renato R.; Costa, Gustavo G.L.; Pereira, Gonçalo Amarante Guimarães

doi:10.1590/s1415-47572007000500032

Cited by 10 publications

(8 citation statements)

References 14 publications

(8 reference statements)

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“…These proteins were subsequently used as keywords to mine the ESTs in the BCGP. Data mining was done using Gene Projects, a sequence management and manipulation system that is part of the LGE bioinformatics platform ( Carazzolle et al , 2007 ). Based on the keywords found, we ran a search that targeted the annotation of each EST in the LGE database.…”

Section: Methodsmentioning

confidence: 99%

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

et al. 2010

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Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and plant defense responses to diseases. The 140 EST-contigs identified through the keyword NBS-LRR were classified according to function. This classification allowed association of the predicted products of EST-contigs with biological processes, including host defense and apoptosis, and with molecular functions such as nucleotide binding and signal transducer activity. Fisher's exact test was used to examine the significance of differences in contig expression between libraries representing the responses to biotic stress challenges and other libraries from the BCGP. This analysis revealed seven contigs highly similar to catalase, chitinase, protein with a BURP domain and unknown proteins. The involvement of these coffee proteins in plant responses to disease is discussed.

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Section: Methodsmentioning

confidence: 99%

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

et al. 2010

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“…Finally, with all the concepts and information on the subject, we can affirm along with some authors (1,6,10,(36)(37) , that informatics, its technologies and tools, such as DM, brought great advantages for the areas that operate voluminous databases.…”

Section: Data Mining Methodsmentioning

confidence: 56%

Técnica de mineração de dados: uma revisão da literatura

Galvão

Marin

2009

Acta paul. enferm.

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The purpose of this study was to conduct a literature review on data mining (DM) technique in the LILACS and SciELO databases and specialized books. A broad data literature search using the words data mining (in English) and/or "mineração de dados" (in Portuguese) and limited to publications between 1999 and 2008, was conducted. The exclusion criteria were the keywords mining industry, mines, mineralogy, and publications that did not describe the methods and the tasks related to data mining. Of 123 publications retrieved, 38 were selected to review. Findings suggest that the existent amount of stored data is titanic and it continue to increase considerably. Thus, the process of knowledge discovery in databases and DM have developed tasks and methods for the retrieval of useful knowledge that may be of interest and necessary for just-in-time decision making in different areas of knowledge. Keywords: Information storage and retrieval/methods; Pattern recognition, automated/methods; Knowledge bases Medical Informatics RESUMOEste artigo teve como objetivo realizar uma revisão da literatura sobre a técnica de mineração de dados (Data Mining -DM) nas bases de dados abrangendo o Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS), Scientific Eletronic Library Online (SCIELO) e alguns livros sobre o tema. Buscou-se uma coleta ampla utilizando as palavras data mining e mineração de dados, abrangendo o período de 1999 a 2008. Como critérios de exclusão foram utilizados os descritores: indústria mineira, minas, mineralogia; foram excluídos artigos que não esclareciam o método e as tarefas relacionadas à mineração de dados. Dos 123 artigos encontrados, 32 foram selecionados. Observou-se que o volume de dados armazenados é gigantesco e continua crescendo exponencialmente. Com isso o processo de Descoberta do Conhecimento em Bases de Dados e DM inclui tarefas e métodos para extração de conhecimento útil, interessante e indispensável na tomada de decisões rápidas nas mais diversas áreas de conhecimento. Descritores: Armazenamento e recuperação da informação/métodos; Reconhecimento automatizado de padrão/métodos; Bases de conhecimento; Informática médica RESUMENEn este artículo se tuvo como objetivo realizar una revisión de la literatura sobre la técnica de mineración de datos (Data Mining -DM) en las bases de datos que abarcaban la Literatura Latino-Americana y del Caribe en Ciencias de la Salud (LILACS), Scientific Eletronic Library Online (SCIELO) y algunos libros sobre el tema. Se buscó una recolección amplia utilizando las palabras data mining y mineración de datos, en el período comprendido entre 1999 a 2008. Como criterios de exclusión fueron utilizados los descriptores: industria minera, minas, mineralogía; se excluyeron artículos que no aclaraban el método y las tareas relacionadas a la mineración de dados. De los 123 artículos encontrados, 32 fueron seleccionados. Se observó que el volumen de datos almacenados es gigantesco y continúa creciendo exponencialmente. Con eso el proceso de Descubri...

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“…Many were implemented for EST analyses and include annotation (Hotz-Wagenblatt et al, 2003) or microarray analyses (Carazzolle et al, 2007), which is outside of our scope. Other tools, such as SABIA or GARSA, must be installed for each project.…”

Section: Discussionmentioning

confidence: 99%

“…A huge amount of automated post-processing programs is available to minimize the bottleneck associated with the increase in data, resulting from new sequencing techniques. Just to name a few, preAssemble (Adzhubei et al, 2006) is helping in the assembly, POSA (Aerts et al, 2004) is a Perl pipeline to automate the assembly, and SABIA (Almeida et al, 2004), GARSA (Dávila et al, 2005), or Gene Projects (Carazzolle et al, 2007) are tools that assist from assembly to annotation. For work with ESTs, different tools were also proposed (Ayoubi et al, 2002;Berezikov et al, 2002;Hotz-Wagenblatt et al, 2003;Mao et al, 2003;Paquola et al, 2003;Matukumalli et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility

Otto

Vasconcellos²,

Gomes³

et al. 2008

Genet. Mol. Res.

113

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AbSTrACT. Optimizing and monitoring the data flow in highthroughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo. pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/.

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Gene projects: a genome web tool for ongoing mining and annotation applied to CitEST

Cited by 10 publications

References 14 publications

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

Técnica de mineração de dados: uma revisão da literatura

ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility

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