Eukaryotic genomes
OPERA LG: efficient and exact scaffolding of large, repeat rich eukaryotic genomes with performance guarantees
... As characteristics of sequencing technologies continue to improve, particularly in read length, assembly quality is also expected to benefit [37, 38]. Recent improvements in protocols for the generation of large mate ...
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An Overview of Nested Genes in Eukaryotic Genomes
... of eukaryotic genomes (5, 8, 9, 13, 32, 48, 49, 62); however, since many antisense sequences may be transcribed as regulatory RNAs, this approach would pre- sumably be less effective for the identification ...
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Estimating translational selection in Eukaryotic Genomes
... more eukaryotic genomes were also analyzed: the orange bread mold (Neurospora crassa), the cryptococ- cosis agent (Cryptococcus neoformans), the malaria para- site (Plasmodium falciparum), the mouse-ear ...
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Empowering the detection of ChIP seq “basic peaks” (bPeaks) in small eukaryotic genomes with a web user interactive interface
... The objective of the bPeaks App is to empower the use of bPeaks, an efficient peak-caller in small eukaryotic genomes. With its docker, there is no need to worry about installing R and the necessary ...
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Comparative Analysis of the Exon Intron Structure in Eukaryotic Genomes
... 72 eukaryotic organisms, including plants, fungi and ...among eukaryotic genomes and revealed some li- neage-specific features of eukaryotic ...of eukaryotic genomic organization ...
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MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes
... Methods: In this paper, we proposed a novel tool MiteFinderII, which was adapted from our previous algorithm MiteFinder, to efficiently detect MITEs from genomics sequences. It has six major steps: (1) build K-mer Index ...
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Repbase Update, a database of repetitive elements in eukaryotic genomes
... In eukaryotic genomes, most TEs exist in families of vari- able sizes, i.e., TEs of one specific family are derived from a common ancestor through its major burst of multiplica- tion in the evolutionary ...
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Genomes in space and time : insights into the functional three dimensional organization of prokaryotic and eukaryotic genomes in response to environmental stimuli and cell cycle progression : a thesis presented in partial fulfilment of the requirements for the degree of Doctorate in Philosophy in Genetics at Massey University, Albany, New Zealand
... of eukaryotic genomes into multiple linear chromosomes results in four major challenges related to the regulation of chromosome replication and segregation, not encountered in circular bacterial ...
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Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
... Here, we take a discrete approach to the problem of TPR violations and we develop an algorithm for the inference of most probable TPR consistent assignments using per-GO term probabilities as input. To the best of our ...
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Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes
... two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) ...prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against ...
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Organization and evolution of information within eukaryotic genomes.
... Chaperonin-60 is a molecular chaperone essential for the folding and assembly of proteins and protein com plexes in all eubacteria and in the plastids and mitochon dria o f eukaryotes. The gene encoding chaperonin-60 ...
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The diversification of PHIS transposon superfamily in eukaryotes
... without any other domain, the other ORF encoding a DNA-binding protein with a Myb/SANT domain. We identified 11 potential active families in the eukaryotic genomes because these TEs contain the two intact ...
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Selection in the evolution of gene duplications
... terial genomes, six archaeal genomes and three mammalian genomes were combined into three kingdom-specific datasets; the remaining eukaryotic genomes were analyzed ...
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Phylogenetic and Variant Analysis of 1,040 SARS-CoV-2 Genomes
... to eukaryotic genomes, it is known that recombination between strains is a key contributor to coronavirus evolution (Graham and Baric, 2010;Li et ...
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Length and Sequence Heterozygosity Differentially Affect HRAS1 Minisatellite Stability During Meiosis in Yeast
... Minisatellites, one of the major classes of repetitive DNA sequences in eukaryotic genomes, are stable in somatic cells but destabilize during meiosis. We previously established a yeast model system by ...
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Clusters of co expressed genes in mammalian genomes are conserved by natural selection
... 2000). These co-expressed genes cannot be operons, because the two genes often occur on opposite strands of DNA, mak- ing polycistronic transcription impossible (Cohen et al., 2000). The same co-expression of neighboring ...
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Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes
... within eukaryotic genomes had the typical traits of transposable elements or multiple repeat sequences (see ...into eukaryotic genomes (43, ...
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The dynamic intein landscape of eukaryotes
... of eukaryotic inteins, we surveyed genomic sequences using BLASTp and previously developed pipelines [31, ...11,001 eukaryotic genomes available through the National Center for Biotechnology ...
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ALUminating the path of atherosclerosis progression: chaos theory suggests a role for Alu repeats in the development of atherosclerotic vascular disease
... enhancer. Ichiyanagi, K., Transposable elements in eukaryotic genomes: epigenetic regulation by the host and functionalization for the host. H., Alu repeats as transcriptional[r] ...
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The human phylome
... sequenced eukaryotic genomes, we have developed a fully automated pipeline (Figure 1) to recon- struct the phylogenies of every protein encoded in the human genome and its homologs in 39 eukaryotic ...
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