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 parti

SUBMITTER: Fang G 

PROVIDER: S-EPMC549560 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature