Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system.

Diener SE, Houfek TD, Kalat SE, Windham DE, Burke M, Opperman C, Dean RA
BMC Bioinformatics. 2005 6: 147

PMID: 15958161 · PMCID: PMC1181624 · DOI:10.1186/1471-2105-6-147

BACKGROUND - Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists.

RESULTS - Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require.

CONCLUSION - This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists.

MeSH Terms (15)

Algorithms Chromosomes, Artificial, Bacterial Cluster Analysis Computational Biology Computer Graphics Database Management Systems Databases, Genetic Expressed Sequence Tags Gene Expression Profiling Information Storage and Retrieval Internet Programming Languages Sequence Analysis Software User-Computer Interface

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