BOV - a web-based BLAST output visualization tool

Description:

Article discussing research on BOV, a web-based BLAST output visualization tool.

Creator(s):
Creation Date: September 15, 2008
Partner(s):
UNT College of Arts and Sciences
Collection(s):
UNT Scholarly Works
Usage:
Total Uses: 149
Past 30 days: 22
Yesterday: 0
Creator (Author):
Gollapudi, Rajesh

Indiana University

Creator (Author):
Revanna, Kashi V.

University of North Texas; Indiana University

Creator (Author):
Hemmerich, Chris

Indiana University

Creator (Author):
Schaack, Sarah

Indiana University

Creator (Author):
Dong, Qunfeng

University of North Texas; Indiana University

Publisher Info:
Publisher Name: BioMed Central Ltd.
Place of Publication: [London, United Kingdom]
Date(s):
  • Creation: September 15, 2008
Description:

Article discussing research on BOV, a web-based BLAST output visualization tool.

Degree:
Department: Biological Sciences
Note:

Abstract: Background: The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. The authors have developed a web-based program, BLAST Output Visualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results: Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion: BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations.

Physical Description:

6 p.

Language(s):
Subject(s):
Keyword(s): output visualization tools | blast output visualization | BOV | genomic research
Source: BMC Genomics, 2008, London: BioMed Central Ltd.
Partner:
UNT College of Arts and Sciences
Collection:
UNT Scholarly Works
Identifier:
  • DOI: 10.1186/1471-2164-9-414
  • ARK: ark:/67531/metadc77114
Resource Type: Article
Format: Text
Rights:
Access: Public
Citation:
Publication Title: BMC Genomics
Volume: 9
Issue: 414
Pages: 6
Peer Reviewed: Yes