MannDB - A microbial database of automated protein sequence analyses and evidence integration for protein characterization

	MannDB - A microbial database of automated protein sequence analyses and evidence integration for protein characterization

About MannDB

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. The data schema is implemented as an Oracle 10g relational database. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS (USDA), CDC, HHS, NIAID, USDA, USFDA, and WHO.

How to use MannDB

1. MannDB is a genome-centric database containing comprehensive automated sequence analysis predictions for protein sequences. Using the browser tool, the user can select a proteome of interest and link to the list of proteins. For large proteomes, proteins are listed in groups of 100, in the order they occur on the genome. The user may then select a protein of interest and link to that protein's sequence analysis reports.

2. A blast tool allows the user to blast a sequence of interest against MannDB to pull up related entries and associated data.

3. A search tool allows the user to search in several ways. First, the user selects a proteome of interest. Then, a search can be constructed using an arbitrary number of search terms, corresponding to sequence analysis results. Searches can be performed as the union ("or") or intersection ("and") of multiple search terms. Literal free-text searches are performed against database text fields. If the current search capabilities are not adequate for your needs, please contact us at ppi group and we will be happy to assist you.

4. Reports and result sets can be downloaded to an Excel spreadsheet.

See the Reports page for more information about sequence analysis reports.

For information/concerns on this page or tool-set, or to make suggestions regarding usability, contact PPI Group

LLNL Disclaimers
UCRL-WEB-219375