Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences

Synonyms

CD-HIT is a fast program for clustering large amount of protein and nucleotide sequences

Definition

Sequence clustering is a process to group sequences into groups (clusters) such that similar sequences are clustered together and can be potentially represented by a single representative sequence. CD-HIT uses a greedy incremental clustering algorithm enhanced by an efficient word filtering heuristics and an effective parallelization technique to do clustering on big sequence datasets efficiently.

Introduction

Since the development of high-throughput sequencing technologies, the amount of available biological sequences has increased dramatically and continues to increase rapidly. Efficient handling and effective analysis of such massive amount of data has become one of the major issues and challenges in many sequencing-based research. Such challenges are typically dominated by two factors: huge data size and high sequence redundancy. Sequence clustering is a key technique that...