No abstract

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.

The longest common subsequence (LCS) problem is a classical problem in computer science. The semi-local LCS problem is a generalisation of the LCS problem, arising naturally in the context of string comparison. In this work, we present a number of algorithmic techniques related to the semi-local LCS problem, and give a number of algorithmic applications of these techniques. Summarising the presented results, we conclude that semilocal string comparison turns out to be a useful algorithmic plug-in, which unifies, and often improves on, a number of previous approaches to various substring-and subsequence-related problems.