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Exploiting Codon-Triplets Association for Genome Primary Structure Analysis

José P. Lousado, Gabriela R. Moura, Manuel A. S. Santos, José Luis Oliveira
2008 2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies  
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

Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo, Adolfo Saiardi
2016 Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies  
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

MIRUNA MIHAELA MICHEU, NICOLETA M. POPA-FOTEA, NICOLETA OPRESCU, MARIA DOROBANTU, ATTILA CRISTIAN RATIU, ALEXANDRU AL. ECOVOIU
2019 Romanian Biotechnological Letters  
., 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

Alexander Bolshoy
2018 Linguistic Frontiers  
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

Susanta K. Behura, David W. Severson
2012 Biological Reviews  
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)

David C. Lamb, Tove Skaug, Hong-Lin Song, Colin J. Jackson, Larissa M. Podust, Michael R. Waterman, Douglas B. Kell, Diane E. Kelly, Steven L. Kelly
2002 Journal of Biological Chemistry  
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

Stephanie Bechtel, Heiko Rosenfelder, Anny Duda, Christian Schmidt, Ute Ernst, Ruth Wellenreuther, Alexander Mehrle, Claudia Schuster, Andre Bahr, Helmut Blöcker, Dagmar Heubner, Andreas Hoerlein (+7 others)
2007 BMC Genomics  
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

M Kozak
1983 Microbiological reviews  
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

M Kozak
1983 Microbiological reviews  
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]

Abhijeet Bakre, Ralph A. Tripp
2018 Gene Expression and Regulation in Mammalian Cells - Transcription Toward the Establishment of Novel Therapeutics  
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

Hongwei Wang, Yan Wang, Zhi Xie
2017 Briefings in Bioinformatics  
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

T A Brown, R W Davies, J A Ray, R B Waring, C Scazzocchio
1983 EMBO Journal  
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

Stephen CJ Parker, Thomas D Tullius
2011 Current Opinion in Structural Biology  
, 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

B. F. Lang, M. Jakubkova, E. Hegedusova, R. Daoud, L. Forget, B. Brejova, T. Vinar, P. Kosa, D. Fricova, M. Nebohacova, P. Griac, L. Tomaska (+2 others)
2014 Proceedings of the National Academy of Sciences of the United States of America  
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

Howard Gamper, Haixing Li, Isao Masuda, D. Miklos Robkis, Thomas Christian, Adam B. Conn, Gregor Blaha, E. James Petersson, Ruben L. Gonzalez, Ya-Ming Hou
2021 Nature Communications  
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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