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Exploiting Codon-Triplets Association for Genome Primary Structure Analysis
2008
2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies
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We have developed a software application for large-scale analysis of codon-triplet associations to shed new light into this problem. ...
The developed algorithms identify codon-triplets context biases, allowing for large scale comparative codon-triplet analysis and for identification of alterations to the standard genetic code. ...
genome primary structure. ...
doi:10.1109/biotechno.2008.21
dblp:conf/biotechno/LousadoMSO08
fatcat:vz4iqgfferbbpnfg5djudy4nua
Discovering New Proteins in Plant Mitochondria by RNA Editing Simulation
2016
Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies
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Therefore common software tools for gene search, successfully applied to find canonical genes, often fail in discovering genes encrypted in the genome of plants. ...
In particular, we consider c → u substitutions leading to the creation of new start and stop codons in the mitochondrial DNA of a given input organism. ...
Although ORF sequences can be easily searched for in a genomic sequence by exploiting one of the existing software tools, such as for example ORF FINDER and STARORF. ...
doi:10.5220/0005664901820189
dblp:conf/biostec/FassettiGLPRS16
fatcat:ubyk4acig5hopajpfbbndd73zy
NGS data validated by Sanger sequencing reveal a puzzling small deletion of MYBPC3 gene associated with hypertrophic cardiomyopathy
2019
Romanian Biotechnological Letters
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., NGS data validated by Sanger sequencing reveal a puzzling small deletion of MYBPC3 gene associated with hypertrophic cardiomyopathy. ...
Bioinformatics analysis revealed a deletion previously reported as c.2441_2443delAGA, but the precise breakpoints mapping appears to be difficult to conclude. ...
For variants classification in terms of clinical significance, we used the criteria issued in 2015 by American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG ...
doi:10.25083/rbl/24.1/91.99
fatcat:efhll6ntyzetfh5bwc7uogquom
Towards an Encyclopaedia of Sequence Biology
2018
Linguistic Frontiers
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Let us check the goals and structure of genomic corpora. ...
Principles of genomic corpus should be discussed and defined, and here, it is my primary contribution to these issues. ...
Complete motif analysis has the potential to be a key tool for experimental and diagnostic genomics": "It is thus becoming increasingly clear that start codon selection is regulated by ¼ sequence/structural ...
doi:10.2478/lf-2018-0003
fatcat:ewn3njfqdjhtxog3hpmmcvzll4
Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes
2012
Biological Reviews
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A. (20076 context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS ONE 2, e847. ...
In the following, we have selected relatively newer studies for discussion on codon bias analysis of insects. ‘hese investigations mostly exploited the whole genome sequence of several insects. ...
doi:10.1111/j.1469-185x.2012.00242.x
pmid:22889422
fatcat:ocpzxfqcmrhujnhx2pr7vmuc4e
The Cytochrome P450 Complement (CYPome) ofStreptomyces coelicolorA3(2)
2002
Journal of Biological Chemistry
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Acknowledgments-We are grateful for comments and advice from Prof. David Hopwood and Dr. David Nelson. ...
Detection of probable CYPs within a genome is facilitated by the presence of consensus sequences within the primary structure that are known to be present in all CYPs. ...
The primary amino acid sequence of CYPs is highly variable, but secondary and tertiary structures are generally conserved as revealed by the known structures. ...
doi:10.1074/jbc.m111109200
pmid:11943767
fatcat:bk52f6dpdnhavi7xhbftxnqsuy
The full-ORF clone resource of the German cDNA Consortium
2007
BMC Genomics
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With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. ...
Conclusion: The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different ...
Acknowledgements We thank Silke Argo for critical reading of the manuscript. ...
doi:10.1186/1471-2164-8-399
pmid:17974005
pmcid:PMC2213676
fatcat:26wvt7fikjhv5iqiss7wn3fzwe
Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles
1983
Microbiological reviews
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Statistical analyses (144) reveal that AUG triplets preceded by appropriately spaced polypurine tracts occur randomly throughout the E. coli genome-i.e., at the level of primary structure, the motif ...
The primary structure of the Saccharomyces cerevisiae gene for alcohol dehydrogenase I. J. Biol. Chem. 257:3018-3025. 29. Bennetzen, J., and B. Hall. 1982. Codon selection in yeast. J. Biol. ...
doi:10.1128/mr.47.1.1-45.1983
fatcat:zpjy33wc75hotfbigodfzr3ul4
Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles
1983
Microbiological reviews
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Statistical analyses (144) reveal that AUG triplets preceded by appropriately spaced polypurine tracts occur randomly throughout the E. coli genome-i.e., at the level of primary structure, the motif ...
The primary structure of the Saccharomyces cerevisiae gene for alcohol dehydrogenase I. J. Biol. Chem. 257:3018-3025. 29. Bennetzen, J., and B. Hall. 1982. Codon selection in yeast. J. Biol. ...
pmid:6343825
pmcid:PMC281560
fatcat:fzaru5gj4bghhbzrd4wnu6hc3m
Viral Modulation of Host Translation and Implications for Vaccine Development
[chapter]
2018
Gene Expression and Regulation in Mammalian Cells - Transcription Toward the Establishment of Novel Therapeutics
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Translation of mRNAs into protein is an essential mechanism of regulating gene expression-and a step exploited by viruses for their own propagation. ...
By tabulating the most frequently used codons in the host genome and comparing to those used in the viral genome, it is possible to discern codon usage bias (CUB) for the virus. ...
Both optimization and deoptimization require extensive computational analysis, which needs to be followed up with measures of attenuation, antigenicity, and structural analysis of the antigen coupled with ...
doi:10.5772/intechopen.72987
fatcat:6cqtg6kf6vdbhkvel6bdd2woie
Computational resources for ribosome profiling: from database to Web server and software
2017
Briefings in Bioinformatics
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Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution. ...
This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. ...
, read extraction for different genomic features and differential analysis. ...
doi:10.1093/bib/bbx093
pmid:28968766
fatcat:uq5zk3rkhvhvlkrbtfjevc5uim
The mitochondnal genome of Aspergillus nidulans contains reading frames homologous to the human URFs 1 and 4
1983
EMBO Journal
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Both URFs were shown by secondary structure predictions to code for predominantly beta-sheeted proteins with strong structural conservation between the fungal and human homologues. ...
These reading frames are 352 and 488 codons in length, and would specify unmodified proteins of mol. wts. 39,000 and 54,000, respectively. ...
Robson for advice and computer facilities during the secondary structure predictions. The work was supported by a project grant from the Medical Research Council to R.W.D and C.S. ...
pmid:11894959
pmcid:PMC555150
fatcat:4pemtmvp2zfzjiqdvwspco5w64
DNA shape, genetic codes, and evolution
2011
Current Opinion in Structural Biology
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, and evolutionary selection for compensatory changes in nucleotide composition that facilitate nucleosome occupancy. ...
While the three-letter genetic code that maps nucleotide sequence to protein sequence is well known, there must exist other codes that are embedded in the human genome. ...
Acknowledgments We thank Adam Woolfe for help in identifying papers reporting exonic enhancers, and Jason A Greenbaum for permission to use Figure 2 . ...
doi:10.1016/j.sbi.2011.03.002
pmid:21439813
pmcid:PMC3112471
fatcat:h3jzq4bqkjh2ldxxxjynvbtcra
Massive programmed translational jumping in mitochondria
2014
Proceedings of the National Academy of Sciences of the United States of America
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hopping | mitochondrial genome | proteome analysis | heterologous expression T he traditional view of translation is that mRNA is read sequentially, one codon at a time. ...
triplet" 50 nt downstream, where translation resumes. ...
In M. capitatus, untranslated codons are exploited as a translation barrier for bypassing undesired sequences. ...
doi:10.1073/pnas.1322190111
pmid:24711422
pmcid:PMC4000857
fatcat:al5db5fv2jbkbnzcbtpfauy5ci
Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA
2021
Nature Communications
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AbstractWhile genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are ...
We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. ...
Mean values and errors for the transition rates and fractional populations determined from modeling with an HMM are reported (for details see "Analysis of smFRET experiments" in Methods). ...
doi:10.1038/s41467-020-20373-z
pmid:33436566
fatcat:wbia5krmgbgz3oa76yjnof37tm
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