Following the theory on regional and national voting, we constructed a regional voting version NN from Pedersen-Nielsen's NN for start codon prediction in nucleotide sequences. Experiments on the TIS data of vertebrate and Arabidopsis thaliana sequences showed improved performances (Matthews correlation coefficients) of 7% and 14% over the original NN.
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http://dx.doi.org/10.1504/IJBRA.2005.007579 | DOI Listing |
Biochemistry
January 2025
Department of Chemistry, University of California, Berkeley, California 94720, United States.
In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation.
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February 2025
Crop Research Unit (Genetics and Plant Breeding), Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal 741252 India.
A protocol for micropropagation of potato ( L.) cv. Cooch Behar local retaining the fidelity of the in vitro regenerants was established for the first time.
View Article and Find Full Text PDFActa Biochim Pol
January 2025
School of Food and Bioengineering, Chengdu University, Chengdu, China.
Members of the families Thermosynechococcaceae and Thermostichaceae are well-known unicellular thermophilic cyanobacteria and a non-thermophilic genus was newly classified into the former. Analysis of the codon usage bias (CUB) of cyanobacterial species inhabiting different thermal and non-thermal niches will benefit the understanding of their genetic and evolutionary characteristics. Herein, the CUB and codon context patterns of protein-coding genes were systematically analyzed and compared between members of the two families.
View Article and Find Full Text PDFCancer Cell Int
January 2025
Institute of Genomic Medicine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Colorectal cancer (CRC) is a major health problem the world face currently and one of the leading causes of death worldwide. CRC is genetically heterogeneous and multiple genetic aberrations may appear on course of the disease throughout patient's lifetime. Genetic biomarkers such as BRAF, KRAS, and NRAS may provide early precision treatment options that are crucial for patient survival and well-being.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Peptide Therapeutics, Genentech, South San Francisco, CA 94080, USA.
mRNA display is an effective tool to identify high-affinity macrocyclic binders for challenging protein targets. The success of an mRNA display selection is dependent on generating highly diverse libraries with trillions of peptides. While translation elongation can canonically accommodate the 61 proteinogenic triplet codons, translation initiation is restricted to the native start codon AUG.
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