Classifying Coding DNA with Nucleotide Statistics
Bioinformatics and Biology Insights, 2009 In this report, we compared the success rate of classification of coding sequences (CDS) vs. introns by Codon Structure Factor (CSF) and by a method that we called Universal Feature Method (UFM).
Nicolas Carels, Diego Frías
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Universal Features for the Classification of Coding and Non-Coding DNA Sequences
Bioinformatics and Biology Insights, 2009 In this report, we revisited simple features that allow the classification of coding sequences (CDS) from non-coding DNA. The spectrum of codon usage of our sequence sample is large and suggests that these features are universal.
Nicolas Carels +2 more
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MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution [PDF]
BMC Bioinformatics, 2006 Background Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are
Johnson Toby +2 more
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The role of highly conserved non-coding DNA sequences in vertebrate development and evolution [PDF]
, 2010 PhDComparisons between vertebrate genome sequences, from mammals to fishes, have revealed thousands of conserved non-coding elements (CNEs) that are associated with developmental genes.
Parker, Hugo
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Investigations of oligonucleotide usage variance within and between prokaryotes. [PDF]
PLoS Computational Biology, 2008 Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di- to tetranucleotides).
Jon Bohlin +2 more
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On the embedding capacity of DNA strands under insertion, deletion and substitution mutations [PDF]
, 2010 Paper presented at Media Forensics and Security XII, SPIE-IS&T Electronic Imaging conference, 18–20 January 2010, San Jose, CaliforniaA number of methods have been proposed over the last decade for embedding information within deoxyribonucleic acid (DNA).
Balado, Félix, Félix Balado
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Fitting Markov property to genetic sequences
Lietuvos Matematikos Rinkinys, 2023 In this paper DNA sequents are modelled as discrete-state Markov chains. Statistical data is presented in contingency tables form. The generalized logit model is used to test the first-order Markov property for all coding and non-coding subsequences of ...
Jurgita Židanavičiūtė +1 more
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Non-coding RNAs and epigenome: de novo DNA methylation, allelic exclusion and X-inactivation [PDF]
The Ukrainian Biochemical Journal, 2013 Non-coding RNAs are widespread class of cell RNAs. They participate in many important processes in cells – signaling, posttranscriptional silencing, protein biosynthesis, splicing, maintenance of genome stability, telomere lengthening, X-inactivation ...
V. A. Halytskiy, S. V. Komisarenko
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Identification of protein coding genes in genomes with statistical functions based on the circular code [PDF]
, 2002 A new statistical approach using functions based on the circular code classifies correctly more than 93 % of bases in protein (coding) genes and non-coding genes of human sequences. Based on this statistical study, a research software called "Analysis of
Lacan, Jérôme +5 more
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Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison [PDF]
, 2006 Non-coding DNA comprises ∼80% of the euchromatic portion of the Drosophila melanogaster genome. Non-coding sequences are known to contain functionally important elements controlling gene expression, but the proportion of sites that are selectively ...
Keightley, Peter, Halligan, Daniel
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