Comparison of Exact String Matching Algorithms for Biological Sequences

Exact matching of single patterns in DNA and amino acid sequences is studied. We performed an extensive experimental comparison of algorithms presented in the literature. In addition, we introduce new variations of earlier algorithms. The results of the comparison show that the new algorithms are efficient in practice.

• Type: Conference
• Year: 2008
• Where: BIRD
• Authors: Petri Kalsi, Hannu Peltola, Jorma Tarhio
• Keywords: Amino Acid Sequences, Bioinformatics, BIRD 2008, Earlier Algorithms, Exact Matching