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

Generalized affine gap costs for protein sequence alignment

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. altschul@ncbi.nlm.nih.gov

|July 22, 1998

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

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Nucleic acids research·2001

Same author

The estimation of statistical parameters for local alignment score distributions.

Nucleic acids research·2001

Same author

SAGEmap: a public gene expression resource.

Genome research·2000

Same author

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.

Bioinformatics (Oxford, England)·2000

Same author

A public database for gene expression in human cancers.

Cancer research·1999

Same author

Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.

Trends in biochemical sciences·1998

Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026

Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026

Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026

Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026

Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026

Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026

See all related articles

This study introduces generalized affine gap costs for protein sequence alignment, improving accuracy by ignoring nonconserved regions. These new costs enhance statistical significance and alignment quality for distantly related proteins.

Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Affine gap costs penalize gap existence and length in sequence alignment.
Conserved residues in proteins often appear in ungapped blocks.
Existing methods struggle with deletions/insertions of multiple residues.

Purpose of the Study:

To propose a generalization of affine gap costs for sequence alignment.
To improve alignment accuracy and statistical significance.
To effectively handle ungapped blocks of conserved residues.

Main Methods:

Developed generalized affine gap cost model.
Empirically analyzed score distributions for local alignments.
Tested alignment accuracy and statistical significance against standard methods.

Related Experiment Videos

Main Results:

Generalized gap costs allow ignoring nonconserved regions.
Score distributions follow an extreme value distribution.
Achieved superior alignments in statistical significance and accuracy.

Conclusions:

Generalized affine gap costs offer improved protein sequence alignment.
This method effectively utilizes conserved residue blocks.
Applicable to both local and multiple sequence alignment problems.