Format

Send to

Choose Destination
BMC Bioinformatics. 2014 May 5;15:128. doi: 10.1186/1471-2105-15-128.

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

Author information

1
Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), University of Oslo, Oslo, Norway. kamran@ibv.uio.no.

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.

PMID:
24885091
PMCID:
PMC4062517
DOI:
10.1186/1471-2105-15-128
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center