Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 7, 459

MannDB - A Microbial Database of Automated Protein Sequence Analyses and Evidence Integration for Protein Characterization

Affiliations

MannDB - A Microbial Database of Automated Protein Sequence Analyses and Evidence Integration for Protein Characterization

Carol L Ecale Zhou et al. BMC Bioinformatics.

Abstract

Background: 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.

Description: MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. 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 when 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, CDC, HHS, NIAID, USDA, USFDA, and WHO.

Conclusion: MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports. Access to MannDB is freely available at http://manndb.llnl.gov/.

Figures

Figure 1
Figure 1
Data flow diagram for MannDB sequence analysis pipeline. External data sources (yellow) are downloaded into MannDB. Software systems (lavender boxes) process and enable display of data. MannDB pipeline manager controls execution of open-source tools (ovals) and blast against MvirDB (green oval).
Figure 2
Figure 2
MannDB database query and browser sample web pages. In this example, user has selected the Campylobacter jejuni proteome (left), entered free text "toxin" (top oval), and checked the MvirDB homology checkbox (bottom oval), resulting in 3 database hits (top right). Selecting single chain protein id 64721 (top right, oval), followed by the "cross-reference" checkbox (middle right, oval) brings up a report page (bottom right) displaying the MvirDB cross reference link (oval).

Similar articles

See all similar articles

Cited by 1 article

References

    1. Slezak T, Kuczmarski T, Ott L, Torres C, Mederos D, Smith J, Truitt B, Mulakken N, Lam M, Vitalis E, Zemla A, Zhou C, Gardner S. Comparative genomics tools applied to bioterrorism defense. Briefings in Bioinformatics. 2003;4:133–149. doi: 10.1093/bib/4.2.133. - DOI - PubMed
    1. Zhou CEZ, Zemla A, Roe D, Young M, Lam M, Schoeinger J, Balhorn R. Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin. Bioinformatics. 2005;21:3085–3096. - PubMed
    1. APHIS Agricultural Select Agent Program select agent and toxin list
    1. CDC bioterrorism agents/diseases list
    1. HHS and USDA select agents and toxins list

Publication types

MeSH terms

LinkOut - more resources

Feedback