Continuing on to some cool applications of Eulerian paths. Intro Visualization GPU/CUDA Injection The goal of this little graph experiment remains exploration of accelerating Eulerian path finding on the GPU. This is the final introductory post. Eulerian Path Hierholzer algorithm works great. It's linear in the number of edges, so as fast as we can … Continue reading Walking the Euler Path: PIN Cracking and DNA Sequencing

# Tag: bioinformatics

# Non-linear Thinking with CUDA.

I love GPU programming for precisely this: it forces and enables you to think about a solution in a non-linear fashion in more than one sense of the word. The Problem Given a set $latex A = \{a_1, a_2 \ldots a_n\}$, output a set $latex S_A = \{0,\ \sum\limits_{k=1}^{n} a_k,\ \sum\limits_{k=i}^{i + j \mod n} … Continue reading Non-linear Thinking with CUDA.

# Motif Finding with Gibbs Sampling (F#)

The Problem "Motif finding is a problem of finding common substrings of specified length in a set of strings. In bioinformatics, this is useful for finding transcription binding sites" (recap here). The problem is succinctly stated on Rosalind. Given a set of strings DNA of size t, find "most common" substrings of length k. "Most common" means, that substrings … Continue reading Motif Finding with Gibbs Sampling (F#)