Deterministic Motif Mining in Protein Databases

Data mining of protein families using common peptides

Predicting the function of a protein from its sequence is typically addressed using sequence-similarity. Here we propose a motif-based approach, using supervised motif extraction from protein sequences belonging to one functional family. The resulting deterministic motifs form Common Peptides (CPs) that characterize this family, allow for data mining of its proteins and facilitate further parti...

Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale

MOTIVATION Protein-protein interaction, mediated by protein interaction sites, is intrinsic to many functional processes in the cell. In this paper, we propose a novel method to discover patterns in protein interaction sites. We observed from protein interaction networks that there exist a kind of significant substructures called interacting protein group pairs, which exhibit an all-versus-all ...

CpG Motif as an Adjuvant in Immunization of a Recombinant Plasmid Encoding Hepatitis C Virus Core Protein

Protein-Based Analysis of Alternative Splicing in the Human Genome

Understanding the functional significance of alternative splicing and other mechanisms that generate RNA transcript diversity is an important challenge facing modern-day molecular biology. Using homology-based, protein sequence analysis methods, it should be possible to investigate how transcript diversity impacts protein structure and function. To test this, a data mining technique ("DiffHit")...

Fast Motif Search in Protein Sequence Databases

Regular expression pattern matching is widely used in computational biology. Searching through a database of sequences for a motif (a simple regular expression), or its variations is an important interactive process which requires fast motif-matching algorithms. In this paper, we explore and evaluate various representations of the database of sequences using suffix trees for two types of query ...