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 statistical theory of sequence alignment with gaps

D Drasdo1, T Hwa, M Lässig

  • 1Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Teltow, Germany. drasdo@imise.uni-leipzig.de

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|October 23, 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

Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data.

mBio·2023
Same author

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.

bioRxiv : the preprint server for biology·2023
Same author

Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations.

Nature communications·2022
Same author

Unraveling liver complexity from molecular to organ level: challenges and perspectives.

Progress in biophysics and molecular biology·2014
Same author

Impact of oxygen environment on mesenchymal stem cell expansion and chondrogenic differentiation.

Cell proliferation·2009
Same author

Comparing the growth kinetics of cell populations in two and three dimensions.

Physical review. E, Statistical, nonlinear, and soft matter physics·2009
Same journal

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). San Diego, California, USA. August 19-23, 2000.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2001
Same journal

Analysis of gene expression data with pathway scores.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Mining for putative regulatory elements in the yeast genome using gene expression data.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Sequence database search using jumping alignments.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
See all related articles

This study presents a statistical theory for local alignment algorithms with gaps. It reveals that sequence correlations cause deviations from scale invariance, which alignment algorithms can detect.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Statistical Modeling

Background:

  • Local alignment algorithms are crucial for sequence analysis.
  • Understanding the statistical properties of these algorithms, especially with gaps, is essential.
  • Previous theories have not fully captured the behavior of alignment statistics under varying conditions.

Purpose of the Study:

  • To develop a quantitative statistical theory for local alignment algorithms incorporating gaps.
  • To describe the linear and logarithmic phases and the phase transition between them.
  • To investigate the relationship between sequence correlations and alignment statistics.

Main Methods:

  • Development of a statistical theory for local alignment.
  • Quantitative analysis of linear and logarithmic phases and phase transitions.

Related Experiment Videos

  • Mathematical modeling of Markov sequences and their correlation properties.

    • Main Results:

    • Demonstrated scale-invariant alignment statistics for Markov sequences without mutual correlations.
    • Quantified deviations from scale invariance as indicators of detectable mutual correlations.
    • Derived conditions for optimal detection of specific mutual sequence correlations.

    Conclusions:

    • The statistical theory provides a framework for understanding local alignment with gaps.
    • Scale invariance is a key property for sequences lacking correlations.
    • Alignment algorithms can effectively detect sequence correlations by observing deviations from scale invariance.