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Related Concept Videos

Improving Translational Accuracy02:07

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 Accuracy02:07

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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Fast Fourier Transform01:10

Fast Fourier Transform

The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
Conservation of Protein Domains02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

Updated: Jun 2, 2026

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
10:03

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy

Published on: June 27, 2014

Improvement in protein-coding region identification based on sliding window trigonometric fast transforms using

Malaya Kumar Hota1, Vinay Kumar Srivastava

  • 1Department of Electronics and Communication Engineering, Motilal Nehru National Institute of Technology, Allahabad 211004, Uttar Pradesh, India. malaya_hota@rediffmail.com

International Journal of Data Mining and Bioinformatics
|April 16, 2011
PubMed
Summary
This summary is machine-generated.

Short-Time Discrete Fourier Transform (ST-DFT) shows superior accuracy in identifying protein-coding DNA regions compared to other trigonometric transforms. Singular Value Decomposition further enhances this identification accuracy.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate identification of protein-coding regions is crucial for understanding gene function and genome annotation.
  • Traditional methods often rely on sequence composition and statistical models.

Purpose of the Study:

  • To evaluate and compare the performance of various sliding window trigonometric fast transforms for identifying protein-coding regions at the nucleotide level.
  • To improve the accuracy of protein-coding region identification using Singular Value Decomposition (SVD).

Main Methods:

  • Analysis of Short-Time Discrete Fourier Transform (ST-DFT), Short-Time Discrete Cosine Transform (ST-DCT), Short-Time Discrete Sine Transform (ST-DST), and Short-Time Discrete Hartley Transform (ST-DHT).
  • Application of Singular Value Decomposition (SVD) on DNA spectra derived from sliding window trigonometric fast transforms.
  • Performance evaluation using the GENSCAN test set and Receiver Operating Characteristic (ROC) curves.

Main Results:

  • ST-DFT demonstrated higher identification accuracy than ST-DCT, ST-DST, and ST-DHT.
  • The proposed method incorporating SVD significantly improved identification accuracy across all tested trigonometric transforms.
  • All trigonometric fast transforms yielded comparable results in terms of area under the ROC curve when SVD was applied.

Conclusions:

  • Sliding window trigonometric fast transforms, particularly ST-DFT, are effective tools for identifying protein-coding regions.
  • SVD is a valuable technique for enhancing the accuracy of these identification methods.
  • The combined approach offers a robust strategy for genomic analysis.