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

ESPSearch: a program for finding exact sequences and patterns in DNA, RNA, or protein.

Terry J Watt1, Donald F Doyle

  • 1Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

Biotechniques
|February 1, 2005
PubMed
Summary

ESPSearch is a powerful bioinformatics tool for identifying DNA and protein sequences. It aids in designing artificial transcription factors and assessing the specificity of small interfering RNA (siRNA) sequences.

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

Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off-target effects.

FEBS open bio·2024
Same author

Endogenous expression of inactive lysine deacetylases reveals deacetylation-dependent cellular mechanisms.

PloS one·2023
Same author

Lysine Deacetylase Substrate Selectivity: Distinct Interaction Surfaces Drive Positive and Negative Selection for Residues Following Acetyllysine.

Biochemistry·2023
Same author

Lysine Deacetylase Substrate Selectivity: A Dynamic Ionic Interaction Specific to KDAC8.

Biochemistry·2021
Same author

Critical review of non-histone human substrates of metal-dependent lysine deacetylases.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·2020
Same author

Chelatable trace zinc causes low, irreproducible KDAC8 activity.

Analytical biochemistry·2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Rapid identification of nucleic acid and amino acid sequences is crucial for various biological research areas.
  • Existing tools may have limitations in handling complex pattern recognition and large-scale sequence analysis.

Purpose of the Study:

  • To introduce ESPSearch, a versatile computer program for sequence identification.
  • To demonstrate the utility of ESPSearch in designing artificial transcription factors and evaluating siRNA specificity.
  • To showcase ESPSearch's capability in identifying specific protein motifs within large proteomes.

Main Methods:

  • ESPSearch utilizes user-constructed databases for simultaneous identification of multiple target sequences, including those with wildcards and mismatches.

Related Experiment Videos

  • The program was employed to identify binding sites for artificial dimeric transcription factors within p53 recognition sites and the BAX gene promoter.
  • Genome-wide and mRNA library searches were performed to estimate the specificity of artificial transcription factors and small interfering RNA (siRNA) sequences.
  • ESPSearch identified proteins with LXXLL motifs from the human proteome using user-defined amino acid groups.

    • Main Results:

    • ESPSearch successfully identified potential binding sites for designed dimeric artificial transcription factors.
    • The specificity of designed transcription factors and potential siRNA sequences was estimated across the human genome and mRNA libraries.
    • Proteins containing various forms of the LXXLL motif were identified from the human proteome.

    Conclusions:

    • ESPSearch is a flexible and efficient tool for diverse sequence and pattern recognition tasks, applicable to both small and large-scale biological data.
    • The program facilitates the design and specificity assessment of novel biological molecules like artificial transcription factors and siRNA.
    • ESPSearch offers a valuable resource for researchers in molecular biology, genomics, and proteomics, with its code freely available.