Dartmouth logo Dartmouth College Computer Science
Technical Report series
CS home
TR home
TR search TR listserv
By author: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
By number: 2017, 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007, 2006, 2005, 2004, 2003, 2002, 2001, 2000, 1999, 1998, 1997, 1996, 1995, 1994, 1993, 1992, 1991, 1990, 1989, 1988, 1987, 1986

Discovery, Visualization and Analysis of Gene Regulatory Sequence Elements in Genomes
Daniel F. Simola
Dartmouth TR2003-456


The advent of rapid DNA sequencing has produced an explosion in the amount of available sequence information, permitting us to ask many new questions about DNA. There is a pressing need to design algorithms that can provide answers to questions related to the control of gene expression, and thus to the structure, function, and behavior of organisms. Such algorithms must filter through massive amounts of informational noise to identify meaningful conserved regulatory DNA sequence elements.

We are approaching these questions with the notion that visualization is a key to exploring data relationships. Understanding the exact nature of these relationships can be very difficult by simply interpreting raw data. The ability to look at data in a graphical form allows us to apply our innate capacity to think visually to discern the subtle relationships that might not be recognizable otherwise.

This thesis provides computational tools to visually identify and analyze candidate motifs in the DNA of a species. This includes a parsing utility to store genomic data and an application to search for and visually identify motifs. Using these tools, novel and previously compiled gene sets were identified using the genome of the plant species Arabidopsis thaliana.

Note: Senior Honors Thesis. Advisor: Jay Aslam.

PDF PDF (3779KB)

Bibliographic citation for this report: [plain text] [BIB] [BibTeX] [Refer]

Or copy and paste:
   Daniel F. Simola, "Discovery, Visualization and Analysis of Gene Regulatory Sequence Elements in Genomes." Dartmouth Computer Science Technical Report TR2003-456, May 2003.

Notify me about new tech reports.

Search the technical reports.

To receive paper copy of a report, by mail, send your address and the TR number to reports AT cs.dartmouth.edu

Copyright notice: The documents contained in this server are included by the contributing authors as a means to ensure timely dissemination of scholarly and technical work on a non-commercial basis. Copyright and all rights therein are maintained by the authors or by other copyright holders, notwithstanding that they have offered their works here electronically. It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author's copyright. These works may not be reposted without the explicit permission of the copyright holder.

Technical reports collection maintained by David Kotz.