Background: The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar protein...
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reas...
In this work we present a new string similarity feature, the sparse spatial sample (SSS). An SSS is a set of short substrings at specific spatial displacements contained in the or...
In this paper we present new approaches to high performance protein database scanning on two novel massively parallel architectures to gain supercomputer power at low cost. The ï¬...
Hidden Markov models (HMMs) are often used for biological sequence annotation. Each sequence feature is represented by a collection of states with the same label. In annotating a ...