A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction
[chapter]
2005
Lecture Notes in Computer Science
Preserved Fulltext
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.)
2021
International Journal of Molecular Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2005
PLoS Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2007
PLoS Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2016
Life
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
1999
Proceedings of the 1999 ACM symposium on Applied computing - SAC '99
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
Frontiers in Bioscience
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2008
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2020
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2000
Research in Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2017
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2008
Genetics and Molecular Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2018
Microbial Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2018
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 851 results