A private DNA motif finding algorithm

Improvement of the Projection Motif Finding Algorithm

In 2001 Buhler and Tompa [BT01] introduced their Projection algorithm for solving the motif discovery problem for motifs of fixed length l. The algorithm finds good candidates for local optimisation by projecting all l-mers present in the input onto a smaller subspace and analysing dense points in that subspace. We have developed Aggregation, a modified version of Projection that analyses dense...

PROJECTION Algorithm for Motif Finding on GPUs

Motif finding is one of the NP-complete problems in Computational Biology. Existing nondeterministic algorithms for motif finding do not guarantee the global optimality of results and are sensitive to initial parameters. To address this problem, the PROJECTION algorithm provides a good initial estimate that can be further refined using local optimization algorithms such as EM, MEME or Gibbs. Fo...

Finding regulatory sequences in DNA: motif discovery

The purpose of motif discovery as discussed here is to find binding sites of DNA binding regulators. We assume that the binding sites are short segments of DNA, not necessarily contiguous, to which a specific (family of) transcription factors can bind. While such sites may appear in genic as well as inter­genic regions, we focus here on finding binding sites only in the promoter region of each ...

CMfinder - a covariance model based RNA motif finding algorithm

MOTIVATION The recent discoveries of large numbers of non-coding RNAs and computational advances in genome-scale RNA search create a need for tools for automatic, high quality identification and characterization of conserved RNA motifs that can be readily used for database search. Previous tools fall short of this goal. RESULTS CMfinder is a new tool to predict RNA motifs in unaligned sequenc...

A Compact Mathematical Programming Formulation for DNA Motif Finding