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

Primer design for large scale sequencing

S Haas1, M Vingron, A Poustka

  • 1Department of Molecular Genome Analysis and Department of Theoretical Bioinformatics,Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. shaas@dkfz_heidelberg.de

Nucleic Acids Research
|June 5, 1998
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

Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity.

Scandinavian journal of immunology·2017
Same author

Electrical impedance tomography for non-invasive assessment of stroke volume variation in health and experimental lung injury.

British journal of anaesthesia·2017
Same author

Does Sacral Nerve Stimulation Improve Continence Through Enhanced Sensitivity of the Anal Canal? A Pilot Study.

Diseases of the colon and rectum·2016
Same author

Increased yield pressure in the anal canal during sacral nerve stimulation: a pilot study with the functional lumen imaging probe.

Neurogastroenterology and motility·2016
Same author

Nurse-led clinics can manage faecal incontinence effectively: results from a tertiary referral centre.

Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland·2015
Same author

Abnormal neuronal response to rectal and anal stimuli in patients with idiopathic fecal incontinence.

Neurogastroenterology and motility·2015
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

PRIDE is a new primer design program that automates primer creation for sequencing projects. Its fuzzy logic and suffix tree system ensure efficient and accurate primer design, especially for large-scale genomics.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Primer design is crucial for DNA sequencing and amplification.
  • Manual primer design can be time-consuming and error-prone.
  • Automated solutions are needed for large-scale sequencing projects.

Purpose of the Study:

  • To introduce PRIDE, a novel automated primer design program.
  • To enhance primer design efficiency and accuracy in sequencing projects.
  • To integrate PRIDE into the Staden package (GAP4) with a graphical user interface.

Main Methods:

  • PRIDE utilizes a fuzzy logic-based system for primer quality assessment.
  • Suffix trees are employed to efficiently store and process large sequencing datasets.
  • The program is integrated into the Staden package (GAP4) for user accessibility.

Related Experiment Videos

Main Results:

  • PRIDE successfully designed 110 sequencing primers and 11 PCR primer pairs.
  • The program demonstrated high performance on genomic templates, cDNAs, and repetitive elements.
  • A high success rate was observed in the test set, indicating PRIDE's reliability.

Conclusions:

  • PRIDE offers a fast, efficient, and user-friendly solution for automated primer design.
  • Its minimal user interaction requirement and fast algorithm are beneficial for large-scale sequencing.
  • PRIDE is a valuable tool for researchers involved in extensive genomics and molecular biology studies.