Performance Analysis of Sequence Alignment Applications

— Recent advances in molecular biology have led to a continued growth in the biological information generated by the scientific community. Additionally, this area has become a multidisciplinary field, including components of mathematics, biology, chemistry, and computer science, generating several challenges in the scientific community from different points of view. For this reason, bioinformatic applications represent an increasingly important workload. However, even though the importance of this field is clear, common bioinformatic applications and their implications on micro-architectural design have not received enough attention from the computer architecture community. This paper presents a micro-architecture performance analysis of recognized bioinformatic applications for the comparison and alignment of biological sequences, including BLAST, FASTA and some recognized parallel implementations of the Smith-Waterman algorithm that use the Altivec SIMD extension to speed-up th...

• Type: Conference
• Year: 2006
• Where: IISWC
• Authors: Friman Sánchez, Esther Salamí, Alex Ramírez, Mateo Valero
• Keywords: Bioinformatic Applications, Common Bioinformatic Applications, IISWC 2006, Operating Systems, Scientific Community