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Related Concept Videos

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...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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.
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...

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Updated: May 23, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

An evolutionary algorithm approach for feature generation from sequence data and its application to DNA splice site

Uday Kamath1, Jack Compton, Rezarta Islamaj-Doğan

  • 1Department of Computer Science, George Mason University, Ashburn, VA 20147, USA. ukamath@gmu.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|April 18, 2012
PubMed
Summary

This study introduces an evolutionary algorithm to automatically generate predictive features from biological sequences, improving machine learning for tasks like DNA splice site prediction.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

  • Bioinformatics and Computational Biology
  • Machine Learning in Genomics

Background:

  • Linking functional information to biological sequences is difficult for machine learning.
  • Current methods rely on pre-defined features or expert knowledge, limiting predictive power.
  • Feature generation from sequence data is a significant challenge in bioinformatics.

Purpose of the Study:

  • To develop an evolutionary algorithm for automated feature generation from sequence data.
  • To enhance the performance of machine learning models in sequence classification tasks.
  • To address the challenge of discovering complex features for accurate biological sequence analysis.

Main Methods:

  • Proposed an evolutionary algorithm to explore large feature spaces for sequence data.
  • Applied the algorithm to the DNA splice site prediction problem.
  • Evaluated generated features using Support Vector Machines for classification.

Main Results:

  • The evolutionary algorithm successfully generated predictive features from DNA sequences.
  • Features derived by the algorithm significantly improved accuracy and precision in splice site prediction.
  • Demonstrated superior performance compared to existing state-of-the-art approaches.

Conclusions:

  • Evolutionary algorithms offer an effective approach for automated feature discovery in biological sequences.
  • This method enhances machine learning model performance for complex tasks like gene finding.
  • The generated features provide a more accurate and precise basis for sequence classification.