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Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif <i>M</i> of length 15, where each planted instance differs from <i>M</i> in 4 positions. Whereas previous algorithms all failed to solve this (15,4)-motif problem. Pevzner and Sze introduced algorithms that… (More)

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose, making use of the… (More)

Following the recent independent proofs of Immerman [SLAM J. nondeterministic space-bounded complexity classes are closed under complementation, two further applications of the inductive counting technique are developed. First, an errorless probabilistic algorithm for the undirected graph s-t connectivity problem that runs in O(log n) space and polynomial… (More)

A fundamental challenge facing biologists is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated. The program YMF identifies good candidates for such binding sites by searching for statistically overrepresented motifs. More specifically, YMF enumerates all motifs in the search space and is… (More)

Understanding the mechanisms that determine the regulation of gene expression is an important and challenging problem. A fundamental subproblem is to identify DNA-binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated, and given the noncoding DNA sequences near those genes. We present an enumerative statistical… (More)

Given a sequence of real numbers ("scores"), we present a practical linear time algorithm to find those nonoverlapping, contiguous subsequences having greatest total scores. This improves on the best previously known algorithm, which requires quadratic time in the worst case. The problem arises in biological sequence analysis, where the high-scoring… (More)

- Martin Tompa
- ISMB
- 1999

This is an investigation of methods for finding short motifs that only occur in a fraction of the input sequences. Unlike local search techniques that may not reach a global optimum, the method proposed here is guaranteed to produce the motifs with greatest z-scores. This method is illustrated for the Ribosome Binding Site Problem, which is to identify the… (More)

Universal traversal sequences for <italic>d</italic>-regular <italic>n</italic>-vertex graphs require length &OHgr;(<italic>d</italic><supscrpt>2</supscrpt><italic>n</italic><supscrpt>2</supscrpt> + <italic>dn</italic><supscrpt>2</supscrpt> log <italic>n/d</italic>), for 3 ≤ <italic>d</italic> ≤ <italic>n</italic>/3 - 2. This is nearly tight for… (More)