The evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement ...

As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the ...

Identifying similarities in large datasets is an essential operation in many applications such as bioinformatics, pattern recognition, and data integration. To make the underlying database system similarity-aware, the core ...

The all-pairs suffix-prefix matching problem is a basic problem in string processing. It has an application in the de novo genome assembly task, which is one of the major bioinformatics problems. Due to the large size of ...

A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination ...