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Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction [chapter]

Antonio Neme, Pedro Miramontes
2005 Lecture Notes in Computer Science  
Another method is proposed here based in rule and tree induction from codon usage of several organisms. It is shown that domain can be identified trough codon usage and a simple set of rules.  ...  Two methods were applied, CN2 and C4.5. Obtained rules describe data better than other methods, in the sense that are topological interpretable and have phenomenological meaning.  ...  The rules obtained by CN2 and the tree obtained by C4.5 are more evidence to show that codon bias is related to biological domain.  ... 
doi:10.1007/978-3-540-25974-9_17 fatcat:g5keviydenbjfbhcswvgqrhh4m

Genome-Wide Identification and Characterization of the Cystatin Gene Family in Bread Wheat (Triticum aestivum L.)

Long He, Xuan Chen, Miaoze Xu, Tingting Liu, Tianye Zhang, Juan Li, Jian Yang, Jianping Chen, Kaili Zhong
2021 International Journal of Molecular Sciences  
The results of codon usage pattern analysis showed that TaCystatins had evident codon usage bias, which was mainly affected by mutation pressure.  ...  Cystatins, as reversible inhibitors of papain-like and legumain proteases, have been identified in several plant species.  ...  of the G and C bases of the codons.  ... 
doi:10.3390/ijms221910264 pmid:34638605 pmcid:PMC8508539 fatcat:naypkx57yvcynmbxij5xo3dfmq

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope

Art F. Y. Poon, Fraser Iain Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
2005 PLoS Computational Biology  
We extend our model to detect interactions between the V3 and C4 domains of the HIV-1 envelope, and account for the uncertainty in mapping substitutions to the tree with a parametric bootstrap.  ...  However, previous studies have relied implicitly on two biologically unrealistic assumptions: (1) that founder effects in the evolutionary history of the sequences can be ignored, and; (2) that statistical  ...  This study was supported by grants from the US National Institutes of Health (NIH grants AI43638, AI47745, AI57167, and AI57167) and a University of California San Diego Centers for AIDS Research (CFAR  ... 
doi:10.1371/journal.pcbi.0030231.eor fatcat:tpv3ukwupzcefi7lb4nn3tjcnq

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope

Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
2007 PLoS Computational Biology  
We extend our model to detect interactions between the V3 and C4 domains of the HIV-1 envelope, and account for the uncertainty in mapping substitutions to the tree with a parametric bootstrap.  ...  However, previous studies have relied implicitly on two biologically unrealistic assumptions: (1) that founder effects in the evolutionary history of the sequences can be ignored, and; (2) that statistical  ...  This study was supported by grants from the US National Institutes of Health (NIH grants AI43638, AI47745, AI57167, and AI57167) and a University of California San Diego Centers for AIDS Research (CFAR  ... 
doi:10.1371/journal.pcbi.0030231 pmid:18039027 pmcid:PMC2082504 fatcat:ocxlhoyimnhhbj3cwreor26iey

Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

J. Wong, Siu-Kin Ng, Wai-Kin Mat, Taobo Hu, Hong Xue
2016 Life  
such self-rARSs were by no means rare occurrences in the RNA World.  ...  such self-rARSs were by no means rare occurrences in the RNA World.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/life6010012 pmid:26999216 pmcid:PMC4810243 fatcat:qgzuunxjxjeehl36teux2itu3m

Exon/intron discrimination using the finite induction pattern matching technique

Pamela Ann Taylor
1999 Proceedings of the 1999 ACM symposium on Applied computing - SAC '99  
The predicted exons are filtered by applying a set of rules. The filtered exons are then grouped into equivalence classes by means of constructing rooted trees to represent gene models.  ...  Finite Induction is applied to the exon and intron components of DNA by building a collection of rules based upon what it finds in the sequences it examines.  ...  Residual for inductive base M using exon filter.  ... 
doi:10.1145/298151.298183 dblp:conf/sac/Taylor99 fatcat:ycf7z4j6izcw7egx6e4alaqnnq

Emergence of life: from functional RNA selection to natural selection and beyond

Jeffery Tze-Fei Wong
2014 Frontiers in Bioscience  
The identification by Woese et al (99) of the three major biological domains of Archaea, Bacteria and Eukarya based on the SSU RNA phylogenetic tree is a landmark in biological science.  ...  Figure 8 . 8 Anticodon usages in standard codon boxes. Usage of any codon in a box is indicated by 1 st anticodon base shown aligned with its complementary codon.  ...  Hannah Hong Xue for valuable discussion, and Dr. Wai-Kin Mat and Xiaofan Ding for expert assistance.  ... 
doi:10.2741/4271 pmid:24896340 fatcat:skchhinyynhhnfqsvmdn256vou

Evolutionary Patterning: A Novel Approach to the Identification of Potential Drug Target Sites in Plasmodium falciparum

Pierre M. Durand, Kubendran Naidoo, Theresa L. Coetzer, Edward Newbigin
2008 PLoS ONE  
EP uses the ratio of non-synonymous to synonymous substitutions (v) to assess the patterns of evolutionary change at individual codons in a gene and to identify codons under the most intense purifying  ...  Parasite and human GK gene sequences were analyzed separately as part of protozoan and metazoan clades, respectively, and key differences in the evolutionary patterns of the two molecules were identified  ...  and suggestions.  ... 
doi:10.1371/journal.pone.0003685 pmid:18997863 pmcid:PMC2577034 fatcat:6uiqgefumfdetppaw6i6wo6p3a

A widespread toxin−antitoxin system exploiting growth control via alarmone signaling

Steffi Jimmy, Chayan Kumar Saha, Tatsuaki Kurata, Constantine Stavropoulos, Sofia Raquel Alves Oliveira, Alan Koh, Albinas Cepauskas, Hiraku Takada, Dominik Rejman, Tanel Tenson, Henrik Strahl, Abel Garcia-Pino (+2 others)
2020 Proceedings of the National Academy of Sciences of the United States of America  
pools, and is counteracted by its HD domain-containing antitoxin.  ...  The toxicity of Cellulomonas marina toxSAS FaRel is mediated by the accumulation of alarmones ppGpp and ppApp, and an associated depletion of cellular guanosine triphosphate and adenosine triphosphate  ...  We are grateful to the Protein Expertise Platform Umeå University and Mikael Lindberg for constructing the plasmids used in this work, Mohammad Roghanian for purifying E. coli RelA, Victoriia Murina for  ... 
doi:10.1073/pnas.1916617117 pmid:32345719 fatcat:subb2jgvmjbt3kppzmpc3m6r4e

Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis

William Nierman, Jonathan A Eisen, Claire M Fraser
2000 Research in Microbiology  
Efforts to make evolutionary sense and biological sense of the gene content of these organisms have been initiated.  ...  Nearly half of the open reading frames identified by these sequencing projects are for potential genes with no known biological function.  ...  The more than two-fold difference in GC content is also reflected in differences in overall codon usage and amino acid composition among species.  ... 
doi:10.1016/s0923-2508(00)00125-x pmid:10865951 fatcat:xmj4vb2qqrdrndoxpyg7nucnva

Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita

Tomokazu Yamazaki, Kensuke Ichihara, Ryogo Suzuki, Kenshiro Oshima, Shinichi Miyamura, Kazuyoshi Kuwano, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Masahira Hattori, Shigeyuki Kawano
2017 Scientific Reports  
The contrasting results were a size range of 200 kb to 4 Mb, lack of clear strata except in Ceratodon, lack of relaxed codon usage bias in Chlamydomonas (but this has not been estimated in some species  ...  The rules governing the generation of these differences are not yet clear. Green seaweeds of the Ulvophyceae are multicellular and grow in coastal areas worldwide 21, 22 .  ...  Masanori Hiraoka of Kochi University for providing the Ulva strains. This study was funded by JSPS KAKENHI (no. 25291070) and MEXT KAKENHI (no. 221S0002) to K.S.  ... 
doi:10.1038/s41598-017-11677-0 pmid:28916791 pmcid:PMC5601483 fatcat:x6uonuds6va7hnay3q6r2evyba

DNATagger, colors for codons

N.M. Scherer, D.M. Basso
2008 Genetics and Molecular Research  
In the next step, the curated datasets were used to estimate the phylogeny of each family, and subsequently to infer the strength of natural selection acting on these proteins.  ...  The main objective of this thesis was to investigate and characterize all PR-families from an evolutionary point of view, using the genetic data available in public databases, to gain insights into the  ...  But they have no biological meaning regarding the function of the gene.Sequence alignments can be structurally based or evolutionary motivated.  ... 
doi:10.4238/vol7-3x-meeting003 fatcat:3erb3dubpjgzjnogoyjctwsla4

No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects

Antoine Danchin, Christos Ouzounis, Taku Tokuyasu, Jean-Daniel Zucker
2018 Microbial Biotechnology  
More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself.  ...  In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules.  ...  Acknowledgements This work was benefited from almost three decades of discussions with members of the INSDC (DDBJ, ENA/ EBI-EMBL and GenBank).  ... 
doi:10.1111/1751-7915.13284 pmid:29806194 pmcid:PMC6011933 fatcat:d47zkrgxdvgofo47n2w562ycvy

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis

Vivien A. C. Schoonenberg, Mitchel A. Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
2018 Genome Biology  
CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts.  ...  Machine learning based on CRISPRO features improves prediction of guide RNA efficacy. The CRISPRO tool is freely available at gitlab.com/bauerlab/crispro .  ...  CRISPRO is platform independent, relies on PyMOL 2.1.0 and is written in Python and R. CRISPRO is released under the GNU AFFERO General Public License v3.0.  ... 
doi:10.1186/s13059-018-1563-5 pmid:30340514 pmcid:PMC6195731 fatcat:5mv6tfirdva65cn47pz4p5esa4

Artificial intelligence and molecular biology

1994 ChoiceReviews  
by the National Library of Medicine.  ...  This work was supported by grant LM04957 from the National Library of Medicine. ARG and DHM are Training Fellows of the National Library of Medicine.  ...  That means that most amino acids are encoded by more than one codon. For example, alanine is represented in DNA by the codons GCT, GCC, GCA and GCG.  ... 
doi:10.5860/choice.31-3826 fatcat:5jmryy7mkbcrvifz6ahlbbdceu
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