System designs to perform bioinformatics sequence alignment

Yilmaz C., GÖK M.

TURKISH JOURNAL OF ELECTRICAL ENGINEERING AND COMPUTER SCIENCES, vol.21, no.1, pp.246-262, 2013 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 21 Issue: 1
  • Publication Date: 2013
  • Doi Number: 10.3906/elk-1105-22
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, TR DİZİN (ULAKBİM)
  • Page Numbers: pp.246-262
  • Keywords: Bioinformatics, sequence alignment, FPGA, LOCAL ALIGNMENT, CLUSTAL, SEARCH
  • Çukurova University Affiliated: Yes


The emerging field of bioinformatics uses computing as a tool to understand biology. Biological data of organisms (nucleotide and amino acid sequences) are stored in databases that contain billions of records. In order to process the vast amount of data in a reasonable time, high-performance analysis systems are developed. The main operation shared by the analysis tools is the search for matching patterns between sequences of data (sequence alignment). In this paper, we present 2 systems that can perform pairwise and multiple sequence alignment operations. Through the optimized design methods, proposed systems achieve up to 3.6 times more performance compared to the previous designs. The proposed systems are modeled with VHDL; these models are simulated and then mapped on a Mezzanine card that contains an FPGA chip. The systolic processing core implemented on the Mezzanine card processes the data obtained from the PC and sends the results back to the PC. The practical functionality of the systems is tested and verified by comparing the system results with pure software results.