A specialized hardware device for the protein similarity search

A. Marongiu, P. Palazzari, V. Rosato

Research output: Contribution to journalArticle

1 Citation (Scopus)


This work presents the architecture of PROSIDIS, a special purpose processor designed to search for the occurrence of substrings similar to a given 'template string' within a proteome. Similarity is determined by means of a weighting matrix which measures the degree of similarity between any two amino acids. The paper recalls the basis of the PHG (Parallel Hardware Generator) tool, developed in the framework of the HADES project (Hardware Design for Scientific Applications). Through PHG it is possible to design, in a nearly automatic way, a parallel hardware which efficiently implements an algorithm described through recurrence equations; PHG is able to generate a synthesizable VHDL which represents a parallel system derived from the System of Affine Recurrence Equations (SARE) describing the problem. In this work we illustrate the advantages derived from designing a special purpose processor to face the protein similarity discovery problem. Some preliminary results are given, reporting the time spent by several conventional computing architectures and by the PROSIDIS processor hosted by a personal computer to solve the same protein analysis problem. The results show that PROSIDIS, implemented on a Xilinx XV1000 FPGA, gives speedup figures ranging from 5.6 up to 55.6. Copyright © 2004 John Wiley & Sons, Ltd.
Original languageEnglish
Pages (from-to)917 - 931
Number of pages15
JournalConcurrency Computation Practice and Experience
Issue number9
Publication statusPublished - 10 Aug 2004
Externally publishedYes


All Science Journal Classification (ASJC) codes

  • Software
  • Theoretical Computer Science
  • Computer Science Applications
  • Computer Networks and Communications
  • Computational Theory and Mathematics

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