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"Junk" DNA Proves to be Highly Valuable1,[object Object],What was once thought of as DNA with zero value in plants--dubbed "junk" DNA--may turn out to be key in helping scientists improve the control of gene expression in transgenic crops.2,[object Object],Cooper and collaborators investigated "junk" DNA in the model plant Arabidopsis thaliana, using a computer program to find short segments of DNA that appeared as molecular patterns…These linked patterns are called pyknons…,[object Object],This discovery in plants illustrates that the link between coding DNA and junk DNA crosses higher orders of biology and suggests a universal genetic mechanism at play that is not yet fully understood. ,[object Object],1-Alfredo Flores, June 2, 2009; http://www.ars.usda.gov/is/pr/2009/090602.htm.,[object Object],2-Bret Cooper, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, USDA.,[object Object]
“Perhaps it is time tobid farewell to the term ‘junk’ DNA – we knew not your true nature.” ,[object Object],(Regulatory RNAs and the demise of ‘junk’ DNA. Genome Biology 2006, 7:328),[object Object],The genome,[object Object],genes,[object Object],Functional elements?,[object Object],Functional Elements: 90%?? 		Junk: 10%??,[object Object],"...a certain amount of hubris was required ,[object Object],for anyone to call any part of the genome 'junk,' ,[object Object],given our level of ignorance."(Francis Collins, 2006),[object Object]
Fig. 1. Pyknons in the 3' UTRs of the apoptosis inhibitor birc4 (shown above the horizontal line) and nine other genes,[object Object],Rigoutsos, Isidore et al. (2006) Proc. Natl. Acad. Sci. USA 103, 6605-6610,[object Object],Copyright ©2006 by the National Academy of Sciences,[object Object]
Welch Wordifier Bosc2009
Welch Wordifier Bosc2009
WordSeekerA Software Suite for Discovery and Characterization of Genomic Words and Genome-Wide Patterns,[object Object]
www.word-seeker.org,[object Object]
word discovery methods,[object Object],sequence-driven,[object Object],(alignment-based),[object Object],pattern-driven,[object Object],(enumerative),[object Object],exhaustive,[object Object],optimized,[object Object],probabilistic,[object Object],optimization,[object Object],deterministic,[object Object],optimization,[object Object],YMF,[object Object],preprocess,[object Object],combine ,[object Object],short patterns,[object Object],AlignAce,[object Object],MEME,[object Object],WINNOWER,[object Object],heuristic,[object Object],exact,[object Object],Teiresias,,[object Object],WordSeeker,[object Object],suffix tree,,[object Object],Weeder,[object Object],GuhaThakurta D., Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res. 2006 Jul 19;34(12):3585-98. Print 2006. Review. ,[object Object],Sandve GK, Drabløs F., A survey of motif discovery methods in an integrated framework. Biol Direct. 2006 Apr 6;1:11.,[object Object]
The WORDIFIER Pattern ,[object Object],for Functional and Regulatory Genomics,[object Object],sequence(s),[object Object],words,[object Object],WORDIFIER,[object Object],scientist,[object Object],scientist,[object Object]
OWEF: An Open Source Word Enumeration Framework for Bioinformatics,[object Object],Kyle Kurz, Lonnie R. Welch, ,[object Object],Frank Drews, Lee Nau, ,[object Object],Jens Lichtenberg,[object Object],Ohio University School of EECS ,[object Object],Bioinformatics Laboratory,[object Object]
Motivation,[object Object],Create a robust Motif Discovery framework using abstracted core algorithms,[object Object],Use a modular design, allowing new methods and algorithms to be implemented quickly and easily,[object Object],Abstract C++ classes,[object Object],Easily extensible,[object Object],Support the Scientific Discovery process,[object Object]
Approach,[object Object]
Project Information,[object Object],Project: ,[object Object],http://bio-s1.cs.ohiou.edu/~wordseek/download/,[object Object],Open Source License: ,[object Object],GNU General Public License (GPL v3),[object Object],Language: ,[object Object],C++,[object Object],Applications:,[object Object],Currently in final testing phase,[object Object],Future Work:,[object Object],Will provide backend for WordSeeker tool at Ohio University and Ohio Supercomputer Center,[object Object],Will be used to fully analyze the Arabidopsis thaliana genome,[object Object]
Open Source Implementation of Batch Extraction for Coding and Non-Coding Sequences,[object Object],Jens Lichtenberg, Lonnie R. Welch,[object Object],Bioinformatics Laboratory,[object Object],School of EECS,[object Object],Ohio University,[object Object]
Motivation,[object Object],Regulatory Genomics tools return and operate on lists of Gene Symbols (e.g. STAT5A, Cd59a, Slc35f4),[object Object],To our knowledge, no currently supported, open source “tool” that allows extraction of specific non-coding sequences for any organism,[object Object],Ensembl API provides limited functionality ,[object Object]
Approach,[object Object],connect to ,[object Object],Ensembl database,[object Object],Input,[object Object],Output,[object Object],Set up repository,[object Object],Retrieve Gene Adaptor,[object Object],create gene object,[object Object],Gene Symbol,[object Object],Retrieve 5’UTR,[object Object],Retrieve 3’UTR,[object Object],Retrieve Exons,[object Object],Retrieve Upstream Adaptor,[object Object],Retrieve Introns,[object Object],Retrieve Promoter,[object Object],Promoter length,[object Object],Output Files,[object Object]
Project Information,[object Object],Project: ,[object Object],http://opensource.msseeker.org,[object Object],GNU General Public License (GPL),[object Object],Language: ,[object Object],Perl,[object Object],Integrated in WordSeeker motif discovery tool of Ohio University Bioinformatics Lab,[object Object],Future Work:,[object Object],Connection to Genbank repository information,[object Object],Release into BioPerl or CPAN,[object Object]
Acknowledgements,[object Object],Thomas Bitterman, OSC,[object Object],Laura Elnitski, NHGRI,[object Object],Susan Evans, OU,[object Object],Matt Geisler, SIU,[object Object],Erich Grotewold , OSU,[object Object],Edwin Jacox, NHGRI,[object Object],Stephen S. Lee, U. Idaho,[object Object],Pooja M. Majmudar, OU,[object Object],Paul Morris, BGSU,[object Object],Chase Nelson, Oberlin,[object Object],Eric Stockinger , OSU,[object Object],Sarah Wyatt, OU,[object Object],Alper Yilmaz, OSU,[object Object],Jeffrey Parvin, OSU,[object Object],Kun Huang, OSU,[object Object],Thomas Mitchell , OSU,[object Object],Kengo Morohashi, OSU,[object Object],Rebecca Lamb , OSU,[object Object],John Finer, OSU,[object Object],[object Object]
Jens Lichtenberg
Rami Alouran
Frank Drews

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