ASAP, a systematic annotation package for community analysis of genomes

Abstract

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future.

Systems approach to refining genome annotation

“…This algorithmic method can be used to direct the search for enzymes and transporters within a genome, and a variety of experimental methods can be used to find and confirm the roles of the responsible genes (7)(8)(9)22). Phenotypic screens of single-deletion mutants have been carried out (18,23), and these will be important for narrowing down likely gene candidates as well as pointing out alternate metabolic routes [requiring the identification of synthetic lethal gene interactions (24)]. Because predictions could be made for only 26 of the 50 cases in this study, a limitation to the computational approach in its current implementation is that the missing reactions must belong to the universal database.…”

“…The algorithm was used iteratively, with each iteration excluding previous solutions, to identify up to 15 possible solutions (13,26). Mutants were identified for phenotypic screens based on literature searches, BLAST sequence-homology searches, context-based homology searches [via the Prolinks database (9)], available Biolog results for E. coli mutants [ASAP database (23)], and unpublished gene-expression microarray data (for L-galactonate).…”

Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays

“…This design provided 1 kb samplings at 60 evenly spaced loci around the chromosome, or about 1% of the genome. A brief description of each of the 60 loci is presented in Table 2, according to the ASAP Database annotation of the EDL933 genome [22]. Note that 1% sampling was chosen to test whether a tiling strategy employing a random sampling of a small portion of a bacterial chromosome could be used to measure diversity within individual strains of E. coli.…”

Community annotation: Procedures, protocols, and supporting tools: Table 1.

“…Organized decentralized community annotation has been used for fungal, archaeal, and prokaryotic genomes (Stover et al 2000;Galagan et al 2002;McLeod et al 2004;Braun et al 2005;Tripathy et al 2006). In addition, several community annotation databases allow ongoing input for fungal and prokaryotic genomes (Glasner et al 2003;D'Ascenzo et al 2004;Winsor et al 2005;Aguero et al 2006;Tripathy et al 2006). Several model organism databases use the Distributed Annotation System (DAS) to facilitate data sharing (Dowell et al 2001), but the DAS system does not yet involve incorporating the community annotation data into an official set of gene models.…”