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

Related Concept Videos

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Per-Unit Sequence Models

Per-Unit Sequence Models

An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Postherpetic Neuralgia: Mechanisms, Risk Factors, and Stratified Management-A Narrative Review.

CNS neuroscience & therapeutics·2026

Same author

Postherpetic neuralgia risk prediction in hospitalised patients with herpes zoster based on MIMIC-IV.

Medicine·2026

Same author

VPS34-mediated autophagosome-lysosome fusion facilitates classical swine fever virus replication.

Journal of virology·2025

Same author

Artificial intelligence in head and neck cancer: a bibliometric and visualization analysis (1995-2025).

Discover oncology·2025

Same author

Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.

Gene·2025

Same author

Spinal Calcrl+ neurons amplify mechanical itch signaling via synaptic plasticity in chronic itch model.

PloS one·2025

Search research articles

Related Experiment Video

Updated: Jun 2, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Markov model to improve word normalization algorithm for biological sequence comparison.

Qi Dai¹, Xiaoqing Liu, Yuhua Yao

¹College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China. daiailiu2004@yahoo.com.cn

|April 21, 2011

Summary

This summary is machine-generated.

This study introduces an improved word normalization technique for biological sequence comparison. It enhances evolutionary analysis by accurately estimating k-word distributions using a Markov model, outperforming existing methods.

More Related Videos

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

Related Experiment Videos

Last Updated: Jun 2, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Statistical measures for biological sequence comparison face challenges with overlapping structures and background word information.
Existing word normalization methods improve performance but assume random base distribution (A, C, T, G).

Purpose of the Study:

To develop an improved word normalization method for biological sequence analysis.
To address the limitations of current normalization techniques by accounting for non-random base distributions.

Main Methods:

Proposed an improved word normalization technique utilizing a Markov model.
Estimated exact k-word distributions based on observed biological sequence data.
Adjusted background information for k-word frequencies in biological sequences.

Main Results:

The improved word normalization method demonstrated higher efficiency in sequence comparison.
Experimental results confirmed the superiority of the Markov model-based approach over existing methods.
The method effectively accounts for the specific background information of biological sequences.

Conclusions:

The proposed Markov model-based word normalization is a more efficient approach for biological sequence analysis.
Accurate estimation of k-word distribution using observed sequence data improves evolutionary analysis.
This method offers a significant advancement in handling background information in sequence comparison.