A DNA Motif Lexicon: cataloguing and annotating sequences.

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 appropriate 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.