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Leaky Scanning02:28

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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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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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
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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...
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Updated: May 24, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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DNA-CBIR: DNA Translation Inspired Codon Pattern-Based Deep Image Feature Extraction for Content-Based Image

Jitesh Pradhan, Hathiram Nenavath

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    DNA data storage enables long-term, high-density information preservation. This study introduces a novel DNA-based Content-Based Image Retrieval (CBIR) method for efficient image searching and recovery from DNA feature vectors.

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    Area of Science:

    • Biotechnology
    • Data Storage
    • Computer Science

    Background:

    • DNA offers a stable, high-density medium for long-term data archival.
    • Current DNA data storage lacks efficient image retrieval mechanisms.

    Purpose of the Study:

    • To develop a novel Content-Based Image Retrieval (CBIR) technique for DNA-based data.
    • To enable efficient searching and retrieval of similar images stored in DNA.

    Main Methods:

    • A novel encoding scheme converts image data into DNA planes using Most-Significant Bits and nucleotide constraints.
    • DNA planes are interpreted via codon sequences for instance-based retrieval.
    • Deep learning architectures (ResNet-50, VGG-16/19, Inception V3) are adapted for classification-based retrieval.

    Main Results:

    • The proposed CBIR technique successfully retrieves similar images from DNA feature vectors.
    • Adaptation to deep learning models facilitates classification-based retrieval tasks.
    • The system demonstrates notable performance improvements across diverse datasets (coral, medical, multi-label).

    Conclusions:

    • The developed DNA-based CBIR method enhances image retrieval efficiency from DNA data storage.
    • This approach offers a significant advancement for managing and accessing multimedia data archived in DNA.
    • The technique shows promise for future applications in DNA data archival and retrieval systems.