Affiliations: Department of Biology, Wheaton College, Norton, MA
02766 USA | Department of Mathematics & Computer Science,
Wheaton College, Norton, MA 02766, USA
Abstract: The rapid proliferation of genomic DNA sequences has created a
significant need for software that can both focus on relatively small areas
(such as within genes or promoters) and provide wide-zoom views of patterns
across entire genomes. We present our DNA Motif Lexicon that enables users to
perform genome-wide searches for motifs of interest and create customizable
results pages, where results differ in the degree and extent of annotation.
Searching for a particular motif is akin to a word search in a natural
language; our motif lexicon speaks to this new time when we will increasingly
rely upon DNA dictionaries that offer rich types of annotation. Indeed, the
concept of "lexomics", introduced in this paper may be appropriate to the
types of meta-analyses relevant to the deciphering of regulatory information.
Currently supporting five genomes, our web-based lexicon allows users to look
up motifs of interest and build user-defined result pages to include the
following: (1) all base pair locations where a motif is found with links to
further search the "neighborhoods" near each of these locations; whether each
location of the motif is genic (within) a gene, intergenic, or a bridging
sequence (overlapping a gene boundary) (2) NCBI hot-links to nearest upstream
and downstream genes for each location (3) statistical information about the
query (4) whether the motif is a certain type of repeat (5) links for the
reverse, complement and reverse-complement of the motif of interest and (6)
hot-links to PubMed abstracts which mention the motif of interest. A software
framework facilitates the continual development of new annotation modules. The
tool is located at: http://genomics.wheatoncollege.edu/cgi-bin/lexicon.exe.
