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BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data

Ralf Stefan Neumann1, Surendra Kumar12, Thomas Hendricus Augustus Haverkamp3 and Kamran Shalchian-Tabrizi1*

Author Affiliations

1 Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), University of Oslo, Oslo, Norway

2 Current address: Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Division of Medicine, Akershus University Hospital, 1478 Akershus, Norway

3 Centre of Ecological and Evolutionary synthesis, Department of Biosciences, University of Oslo, Oslo, Norway

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BMC Bioinformatics 2014, 15:128  doi:10.1186/1471-2105-15-128

Published: 5 May 2014

Abstract

Background

Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data.

Results

Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a user friendly graphical user interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java interface-based plugin structure facilitates the addition of customized third party functionality.

Conclusion

The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.

Keywords:
Analysis; BLAST; High-throughput; Taxonomy; Text-mining; Visualization