Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

A special-purpose processor for gene sequence analysis

B Fagin1, J G Watt, R Gross

  • 1Thayer School of Engineering, Dartmouth College, Hanover, NH 03755.

Computer Applications in the Biosciences : CABIOS
|April 1, 1993
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

New rules on bovine semen production.

The Veterinary record·2004
Same author

A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins.

Journal of bacteriology·1996
Same author

Effects of weekly iron supplementation on pregnant Indonesian women are similar to those of daily supplementation.

The American journal of clinical nutrition·1996
Same author

Adenosine inhibitory effect on enhanced growth of aortic smooth muscle cells from streptozotocin-induced diabetic rats.

British journal of pharmacology·1996
Same author

Signal transduction and virulence regulation in Bordetella pertussis.

Microbiologia (Madrid, Spain)·1996
Same author

Primary health care physicians' treatment of psychosocial problems: implications for social work.

Health & social work·1996
Same journal

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

Computer applications in the biosciences : CABIOS·1998
Same journal

Two applications to facilitate the viewing of database search result files on the Macintosh.

Computer applications in the biosciences : CABIOS·1998
Same journal

BioWish: a molecular biology command extension to Tcl/Tk.

Computer applications in the biosciences : CABIOS·1998
Same journal

The Sequence Alerting Server--a new WEB server.

Computer applications in the biosciences : CABIOS·1998
Same journal

A software tool for the analysis of mass spectrometric disulfide mapping experiments.

Computer applications in the biosciences : CABIOS·1998
Same journal

SAMBA: hardware accelerator for biological sequence comparison.

Computer applications in the biosciences : CABIOS·1998
See all related articles

This study introduces a custom hardware accelerator for gene sequence analysis, significantly improving computational biology performance. The specialized computer achieves a 15-fold speedup for nucleotide sequence alignment using the Needleman-Wunsch algorithm.

Area of Science:

  • Computational biology
  • Computer architecture
  • Bioinformatics hardware

Background:

  • Advances in computational biology are hindered by a knowledge gap between molecular biologists and computer designers.
  • Special-purpose computers offer significant cost/performance advantages over general-purpose machines for specific computational tasks.

Purpose of the Study:

  • To address the scarcity of hardware designs for biological computing.
  • To develop a custom accelerator for accelerating gene sequence analysis.

Main Methods:

  • Implementation of a specialized computer using TTL and FPGA technology.
  • The accelerator utilizes the Needleman-Wunsch algorithm for nucleotide sequence alignment.
  • The system is built on two NuBus boards connected to a Mac IIf/x, clocked at 10 MHz.

Related Experiment Videos

Main Results:

  • The custom accelerator is fully functional and demonstrated.
  • Achieved a 15-fold performance improvement compared to an unassisted host system.
  • Sequence length is limited only by available memory, with a product of lengths up to 2^22.

Conclusions:

  • Custom hardware accelerators can bridge the knowledge gap and enhance biological computing.
  • The developed accelerator provides a significant performance boost for gene sequence analysis.
  • This approach highlights the potential for specialized hardware in accelerating complex biological computations.