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

Compression of protein sequence databases

V B Strelets1, H A Lim

  • 1Computational Genetics and Biophysics, Supercomputer Computations Research Institute, Florida State University, Tallahassee 32306-4052, USA.

Computer Applications in the Biosciences : CABIOS
|October 1, 1995
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

Diagnosis of Schizophrenia Based on the Data of Various Modalities: Biomarkers and Machine Learning Techniques (Review).

Sovremennye tekhnologii v meditsine·2023
Same author

[The Association of Brain-Derived Neurotrophic Factor and Serotonin Transporter Genes with the Parameters of Early Event-Related Potentials During the Passive Perception of Words].

Zhurnal vysshei nervnoi deiatelnosti imeni I P Pavlova·2019
Same author

[Perception of Verbal Stimuli in the Norm and in Schizophrenia].

Zhurnal vysshei nervnoi deiatelnosti imeni I P Pavlova·2019
Same author

The burden of filial piety: A qualitative study on caregiving motivations amongst family caregivers of patients with cancer in Singapore.

Psychology & health·2016
Same author

[The Influence of Threatening Stimuli on the Component P200 in Patients with Paranoid Schizophrenia].

Fiziologiia cheloveka·2015
Same author

[Latencies of Sensory and Cognitive Components of Event Related Potentials during Perception of Verbal Stimuli in the Norm and Schizophrenic Patients].

Zhurnal vysshei nervnoi deiatelnosti imeni I P Pavlova·2015
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

We developed a novel algorithm to compress the Protein Information Resource (PIR) database, creating a compact databank for researchers with limited storage. This tool offers fast, direct access to sequence data and supports standard queries, even on personal computers.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Database Management

Background:

  • Researchers often face storage limitations when working with large biological sequence databases like PIR.
  • Existing methods for accessing PIR data may require significant storage or network access, hindering individual researchers and developers.

Purpose of the Study:

  • To develop a space-efficient algorithm for compressing the PIR database.
  • To create a C-based interface for fast, direct access to compressed PIR data without extensive decompression.
  • To enable standalone use of PIR data on personal computers and UNIX systems.

Main Methods:

  • An alignment-based algorithm was developed for compressing protein sequences.
  • The PIR database was restructured into separate file sets for modularity.

Related Experiment Videos

  • A C language interface was implemented to support standard PIR queries and direct programmatic access.

    • Main Results:

    • A compact PIR databank, SAGITTARIUS PIR, was created, significantly outperforming ZIP compression for protein sequences.
    • The C interface allows direct data retrieval from PIR without network dependency or full decompression.
    • The system supports standard PIR queries and offers additional features like homology searches on PC-compatibles.

    Conclusions:

    • The SAGITTARIUS PIR package provides an efficient solution for researchers needing to access PIR data with limited storage.
    • The developed compression algorithm and access interface enhance the usability of biological sequence databases on diverse computing platforms.
    • This tool empowers individual researchers and software developers by offering flexible and fast access to critical sequence information.