Open Access Software

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

Stephen E Diener1, Thomas D Houfek2, Sam E Kalat2, DE Windham1, Mark Burke2, Charles Opperman2 and Ralph A Dean1*

Author Affiliations

1 Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA

2 Plant Nematode Genetics Group, North Carolina State University, Raleigh, NC 27695, USA

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BMC Bioinformatics 2005, 6:147  doi:10.1186/1471-2105-6-147

Published: 15 June 2005

Abstract

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.