Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Methods for calculating the probabilities of finding patterns in sequences.

¹MRC Laboratory of Molecular Biology, Cambridge, UK.

Computer Applications in the Biosciences : CABIOS

|April 1, 1989

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

Protein disk of tobacco mosaic virus at 2.8 A resolution showing the interactions within and between subunits.

Nature·2009

Same author

Sequence assembly and finishing methods.

Methods of biochemical analysis·2001

Same author

The Staden package, 1998.

Methods in molecular biology (Clifton, N.J.)·1999

Same author

An oligo-screening strategy to fill gaps found during shotgun sequencing projects.

DNA sequence : the journal of DNA sequencing and mapping·1999

Same author

Both DNA strands of antibody genes are hypermutation targets.

Proceedings of the National Academy of Sciences of the United States of America·1998

Same author

Automated detection of point mutations using fluorescent sequence trace subtraction.

Nucleic acids research·1998

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 probability-generating functions to calculate motif probabilities in biological sequences. These methods aid in identifying patterns and their components within DNA and protein data.

Area of Science:

Bioinformatics
Computational Biology
Sequence Analysis

Background:

Identifying recurring patterns (motifs) in biological sequences is crucial for understanding function.
Current methods may lack robust probabilistic frameworks for motif discovery.

Purpose of the Study:

To present a probabilistic approach for calculating motif occurrence in nucleic acid and protein sequences.
To define and analyze higher-level structures termed 'patterns' composed of motifs.

Main Methods:

Utilizing probability-generating functions to derive equations for motif probabilities.
Developing algorithms for calculating probabilities across nine motif definitions.
Defining 'patterns' as ordered lists of motifs with specified spacing ranges.

Related Experiment Videos

Deriving equations for expected pattern matches.

Main Results:

Successfully calculated probabilities for various motif definitions.
Demonstrated comparisons with random sequence searches.
Provided a framework for analyzing patterns, including motif spacing.

Conclusions:

Probability-generating functions offer a powerful tool for motif and pattern analysis in sequence data.
The developed methods enhance the statistical rigor of motif discovery in bioinformatics.