CONCURRENT BIOINFORMATICS SOFTWARE FOR DISCOVERING GENOME-WIDE PATTERNS AND WORD-BASED GENOMIC SIGNATURES Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al-Ouran, Lev Neiman, Lee Nau, Joshua Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank Drews, Stephen Lee, Lonnie Welch
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Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al-Ouran, Lev Neiman, Lee Nau, Joshua Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank Drews, Stephen Lee, Lonnie Welch
The WordSeeker Tool
Enumeration Suffix Tree and Suffix Array Radix Tree
Scoring Clustering
Sequence Clustering Word Clustering
Conservation Analysis Phast Cons Score Extraction
Location Distributions Sequence Coverage
Min set of words necessary tocover all sequences
Module Discovery Enumerative
Ranger Markup Basic Functional Elements
Software Properties
Google code repository: http://code.google.com/p/word-seeker/ GNU General Public License v3 Doxygen code generator (Internal Documentation). Svn for command line access: http://word-seeker.googlecode.com/svn/trunk
Requirements G++ compiler version 4.1* or higher OpenMP headers MPI environment (distributed version) For visualizations and other post-processing steps
Perl 5.8.8, TFBS (http://tfbs.genereg.net/) SET::Scalar LWP::Simple Parallel::Forkmanager GD::Graphs::bars, Algorithm::Cluster Bio::SeqIO (all available through CPAN) Gnuplot version 4.2 or higher