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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Evolutionary Relationships through Genome Comparisons02:54

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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Synteny and Evolution02:31

Synteny and Evolution

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Updated: May 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Discovering weighted patterns in intron sequences using self-adaptive harmony search and back-propagation algorithms.

Yin-Fu Huang1, Chia-Ming Wang, Sing-Wu Liou

  • 1Department of Computer Science and Information Engineering, National Yunlin University of Science and Technology, Douliu, Yunlin 640, Taiwan. huangyf@yuntech.edu.tw

Thescientificworldjournal
|June 6, 2013
PubMed
Summary
This summary is machine-generated.

A novel hybrid system discovers significant weighted patterns in human intron sequences. These patterns improve the specificity of splice site recognition, aiding genetic analysis.

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Published on: March 29, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Human intron sequences contain regulatory elements crucial for gene expression.
  • Identifying specific patterns in introns, like splice sites, is vital for understanding gene splicing.
  • Existing models for intron patterns can be ambiguous, necessitating improved analytical methods.

Purpose of the Study:

  • To develop and evaluate a hybrid system for discovering weighted patterns in human intron sequences.
  • To assess the significance of these weighted patterns using a machine learning classifier.
  • To compare the discovered patterns with established intron consensus models for improved accuracy.

Main Methods:

  • A hybrid self-adaptive harmony search and back-propagation mining system was employed.
  • Weighted patterns were identified within human intron sequences.
  • A lazy nearest neighbor classifier was used to test the significance of the discovered weights.
  • The discovered weighted patterns were compared against the popular intron consensus model.

Main Results:

  • The hybrid system successfully identified significant weighted patterns in human intron sequences.
  • Numerical results confirmed the importance of these weighted patterns.
  • The discovered weighted patterns enhanced the specificity of the 5' splice site (5SS) and 3' splice site (3SS) header patterns.
  • Ambiguous consensus models were refined into more concrete representations.

Conclusions:

  • The proposed hybrid system is effective for discovering meaningful weighted patterns in genomic sequences.
  • Weighted patterns offer a more precise approach to identifying functional elements like splice sites.
  • This method advances the analysis of human intron sequences and splice site recognition.