JunctionViewer: customizable annotation software for repeat-rich genomic regions

Description

JunctionViewer generates concise graphical representations of DNA sequence features using NCBI BLAST/WU-BLAST, cross_match, and MUMmer, as well as customizable annotation data. Results are displayed through the graphical interface or can be viewed from PostScript® output. It is particularly suited for annotating repeat-rich genomic regions, such as centromeres. The name "JunctionViewer" stems from the software's original purpose - visualizing "repeat junctions" in the centromeres of maize (Luce et al., 2006).

For more details and if you use this software please refer to the related publication:
Wolfgruber T, Presting G (2010) JunctionViewer: customizable annotation software for repeat-rich genomic regions. BMC Bioinformatics 11: 23. doi:10.1186/1471-2105-11-23. url:http://www.biomedcentral.com/1471-2105/11/23

Features

• User definable parameters for each BLAST/cross_match database.
• Competes all BLAST HSPs/cross_match results between subject databases to reveal only the best results.
• Displays exact sequence matches within query sequence as reported by MUMmer.
• Plots customizable annotation data (e.g., ChIP-Seq mapped reads positions) on top of BLAST/cross_match/MUMmer results.

Usage

1. Run JunctionViewer script without parameters to generate a template parameters file.
2. Populate parameters file (comments are given indicating how this should be done).
3. Run JunctionViewer with parameters file as argument.

Requirements

Perl, Perl modules BioPerl and Tk, NCBI BLAST and/or WU-BLAST, cross_match, and MUMmer.

Downloading

Download the JunctionViewer package through SourceForge.net®. This package includes the software, setup/usage instructions, example files, and license documents:

Running JunctionViewer using example files

1. Install required Perl software/Perl modules by reading the README-linux.txt file if you are using a unix-like OS, or README-windows.txt if you are a Windows user.
2. Obtain at least NCBI BLAST. Linux users may also obtain cross_match and/or MUMmer. If you are unable to get a binary, e.g., cross_match, annotations using that algorithm may be omitted (see step 3).
3. Re-define BLAST/cross_match/MUMmer binary locations in example parameters file where indicated under comment lines "# !!!Change the following to use your own binary location!!!" If you were unable to get a binary, you may also set a binary to no value ("Binary="), which will mean alignments using that binary will be skipped.
4. Run the script with the updated parameters file, i.e., using command line statement 'JunctionViewer-xx.pl JunctionViewer-xx.pl.example_parameters-[linux,windows].txt'.
5. Select a sequence and press "Display single selection" to visualize its features.

Results from example files

GUI	Query sequence #1 ("c0530C10")	Query sequence #2 ("chr2_seqs")

License

GPLv3

Copyright 2010,2009 Thomas K. Wolfgruber