Dataset Information

Specialized microbial databases for inductive exploration of microbial genome sequences.

ABSTRACT: BACKGROUND: The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. METHODS: The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. RESULTS: Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. CONCLUSION: This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison.

SUBMITTER: Fang G

PROVIDER: S-EPMC549560 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature

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Specialized microbial databases for inductive exploration of microbial genome sequences.

Fang Gang G Ho Christine C Qiu Yaowu Y Cubas Virginie V Yu Zhou Z Cabau Cédric C Cheung Frankie F Moszer Ivan I Danchin Antoine A

BMC genomics 20050207

<h4>Background</h4>The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects.<h4>Methods</h4>The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented.<h4>Results< ...[more]

PMID: 15698474

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Project description:BackgroundHealthcare research funders may undertake various roles to facilitate implementation of research findings. Their ability to enact such roles depends on several factors, knowledge of implementation being one essential requirement. However, previous studies do not assess the type or level of knowledge about implementation that research funders possess. This paper therefore presents findings from a qualitative, inductive study of the implementation knowledge of research funders. Three aspects of this knowledge are explored, namely how research funders define implementation, their level of self-assessed implementation knowledge and the factors influencing their self-assessment of implementation knowledge.MethodsResearch funders (n?=?18) were purposefully selected from a sample of research funding organisations in Sweden (n?=?10). In-depth semi-structured interviews were conducted, recorded and transcribed verbatim. An inductive method using a systematic coding procedure was employed to derive the findings.ResultsThe research funders defined implementation as either an outcome or a process, with the majority believing that implementation of healthcare research results demands a process, although its complexity varied in the research funders' view. They perceived their own level of implementation knowledge as either limited or substantial, with a majority regarding it as limited. Clinical research experience, clinical experience and task relevance were singled out as the clearest factors affecting the self-assessment of their own implementation knowledge.ConclusionsThis study, the first to focus on implementation knowledge of research funders, demonstrates that they are a category of policy-makers who may possess knowledge, based on their previous professional experience, that is comparable to some important findings from implementation research. Consequently, the findings not only pinpoint the relevance of professional experience, but also reveal a lack of awareness and knowledge of the results of implementation research among research funders in charge of healthcare research.

Dataset Information

Specialized microbial databases for inductive exploration of microbial genome sequences.

Publications

Specialized microbial databases for inductive exploration of microbial genome sequences.

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