We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algor...

A crucial step in determining solution structures of proteins using nuclear magnetic resonance (NMR) spectroscopy is the process of sequential assignment, which correlates backbone resonances to corresponding residues in the primary sequence of a protein, today, typically using data from triple-resonance NMR experiments. Although the development of automated approaches for sequential assignment...

Recent articles [6, 3, 5, 7] introduce the concept of phase shifting equivalent keys in stream ciphers, and exploit this concept in order to mount attacks on some specific ciphers. The idea behind phase shifting equivalent keys is that, for many ciphers, each internal state can be considered as the result of an injection of a key and initialization vector. This enables speeding up the standard ...

In this paper, we present the first cryptographic preimage attack on the full MD5 hash function. This attack, with a complexity of 2, generates a pseudo-preimage of MD5 and, with a complexity of 2, generates a preimage of MD5. The memory complexity of the attack is 2×11 words. Our attack is based on splice-and-cut and localcollision techniques that have been applied to step-reduced MD5 and othe...

Motivation One of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a 'good enough' solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a 'goo...

Using a strongly typed functional programming language for genetic programming has many advantages, but evolving functional programs with variables requires complex genetic operators with special cases to avoid creating ill-formed programs. We introduce combinator expressions as an alternative program representation for genetic programming, providing the same expressive power as strongly typed ...

Costas and sonar sequences were respectively introduced in [2] and [10] to deal with the following problem: “An object is moving towards (or away) from an observer, who wants to know effectively the distance to the object and its velocity.” The solution to the problem makes use of the Doppler effect, which states the following: when a signal bounces off a moving target its frequency changes in ...