BLAST Output Visualization Tool (BOV) allows users to interactively visualize the BLAST high-scoring segment pairs between query and hit sequences for dissecting complex matching patterns. This software is aimed at facilitating users interested in identifying regions of colinearity, duplication, translocation, and inversion using the BLAST program.

For example, it can be used:

  1. to investigate intron/exon evolution among homologous genes
  2. to identify new spatial alignments, inversions, etc. among duplicate genes
  3. to analyze repetitive elements or tandem arrays
  4. to identify large scale synteny
  5. to assemble contigs based on known scaffolds or other genomes
Description of the Webpages

A. Main page showing input fields for the user's email and single or batch query BLAST output files. The user's email is requested in order to send a separate URL providing access to the BOV output file generated for any given input for 60 days.

B. A summary table of queries, including an individual link to each, is generated when batch query input files are uploaded.

C. All HSPs for a given query and hit sequences are initially displayed with colored lines connecting the start and end positions of each matching region along the sequence.

D. The Zoom function can be used to examine a particular region along the hit or query sequence.

E. The Highlight function, activated by clicking on the column (indicated by the red-circle), changes the graphical display from lines (default) to trapezoids.

F. Pair-wise alignments for individual HSPs can be seen by clicking on the Alignment column for an individual HSP region.

G. The individual query or hit sequence region for each HSP can be viewed by clicking on the appropriate button at the top of the pair-wise alignment window.