scholarly journals Site2genome: locating short DNA sequences in whole genomes

2004 ◽  
Vol 20 (9) ◽  
pp. 1468-1469 ◽  
Author(s):  
M. C. Frith ◽  
A. S. Halees ◽  
U. Hansen ◽  
Z. Weng
Keyword(s):  
Dna Sequences ◽  
Whole Genomes

scholarly journals Model-based inference of punctuated molecular evolution

2019 ◽  
Author(s):  
Marc Manceau ◽  
Julie Marin ◽  
Hélène Morlon ◽  
Amaury Lambert
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Temporal Variations ◽  
Multiple Sequence ◽  
Model Combining ◽  
Constant Rate ◽  
Whole Genomes ◽  
Standard Models ◽  
Natural Variance ◽  
Venom Proteins

AbstractIn standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a time-varying rate (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary time scale. Here, we develop a model combining basal, clock-like molecular evolution with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) co-occurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular evolution and from temporal variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

scholarly journals Model-Based Inference of Punctuated Molecular Evolution

2020 ◽  
Vol 37 (11) ◽  
pp. 3308-3323 ◽  
Author(s):  
Marc Manceau ◽  
Julie Marin ◽  
Hélène Morlon ◽  
Amaury Lambert
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Multiple Sequence ◽  
Model Combining ◽  
Constant Rate ◽  
Whole Genomes ◽  
Standard Models ◽  
Natural Variance ◽  
Venom Proteins ◽  
Relaxed Clock

Abstract In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

scholarly journals Fungi of quarantine concern for China I: Dothideomycetes

2021 ◽  
Author(s):  
P. Zhao ◽  
P.W. Crous ◽  
L.W. Hou ◽  
W.J. Duan ◽  
L. Cai ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Rapid Identification ◽  
Fungal Species ◽  
New Combination ◽  
Helminthosporium Solani ◽  
Whole Genomes ◽  
The One ◽  
One Fungus One Name ◽  
Current List

The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentro­spora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens.

scholarly journals Three novel canine papillomaviruses support taxonomic clade formation

2009 ◽  
Vol 90 (11) ◽  
pp. 2615-2621 ◽  
Author(s):  
Christian E. Lange ◽  
Kurt Tobler ◽  
Mathias Ackermann ◽  
Lucia Panakova ◽  
Keith L. Thoday ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Human Papillomaviruses ◽  
Sequence Alignments ◽  
Conserved Sequence ◽  
Whole Genomes ◽  
Sequence Elements ◽  
Sequence Similarities

More than 100 human papillomaviruses (HPVs) have been identified and had their whole genomes sequenced. Most of these HPVs can be classified into three distinct genera, the alpha-, beta- and gamma-papillomaviruses (PVs). Of note, only one or a small number of PVs have been identified for each individual animal species. However, four canine PVs (CPVs) (COPV, CPV2, CPV3 and CPV4) have been described and their entire genomic sequences have been published. Based on their sequence similarities, they belong to three distinct clades. In the present study, circular viral DNA was amplified from three dogs showing signs of pigmented plaques, endophytic papilloma or in situ squamous cell carcinoma. Analysis of the DNA sequences suggested that these are three novel viruses (CPV5, CPV6 and CPV7) whose genomes comprise all the conserved sequence elements of known PVs. The genomes of these seven CPVs were compared in order properly classify them. Interestingly, phylogenetic analyses, as well as pairwise sequence alignments of the putative amino acid sequences, revealed that CPV5 grouped well with CPV3 and CPV4, whereas CPV7 grouped with CPV2 but neither group fitted with other classified PVs. However, CPV6 grouped with COPV, a lambda-PV. Based on this evidence, allocation of CPVs into three distinct clades could therefore be supported. Thus, similar to HPVs, it might be that the known and currently unknown CPVs are related and form just a few clades or genera.

Feature Selection for the Promoter Recognition and Prediction Problem

2008 ◽  
pp. 2248-2262
Author(s):  
George Potamias ◽  
Alexandros Kanterakis
Keyword(s):  
Feature Selection ◽  
Dna Sequences ◽  
Data Sets ◽  
Prediction Problem ◽  
Hybrid Filter ◽  
Nucleotide Pair ◽  
Promoter Recognition ◽  
Whole Genomes ◽  
Computational Discovery ◽  
Algorithmic Process

With the completion of various whole genomes, one of the fundamental bioinformatics tasks is the identification of functional regulatory regions, such as promoters, and the computational discovery of genes from the produced DNA sequences. Confronted with huge amounts of DNA sequences, the utilization of automated computational sequence analysis methods and tools is more than demanding. In this article, we present an efficient feature selection to the promoter recognition, prediction, and localization problem. The whole approach is implemented in a system called MineProm. The basic idea underlying our approach is that each position-nucleotide pair in a DNA sequence is represented by a distinct binary-valued feature—the binary position base value (BPBV). A hybrid filter-wrapper, featuredeletion (or addition) algorithmic process is called for in order to select those BPBVs that best discriminate between two DNA sequences target classes (i.e., promoter vs. nonpromoter). MineProm is tested on two widely used benchmark data sets. Assessment of results demonstrates the reliability of the approach.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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