The Experts below are selected from a list of 33543 Experts worldwide ranked by ideXlab platform

Ann B. Jacobson - One of the best experts on this subject based on the ideXlab platform.

  • ‘Well-determined’ regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA
    Nucleic Acids Research, 1995
    Co-Authors: Michael Zuker, Ann B. Jacobson
    Abstract:

    Recent structural analyses of genomic RNAs from RNA coliphages suggest that both well-determined base paired helices and well-determined structural domains that are identified by "energy Dot Plot" analysis using the RNA folding package mfold, are likely to be predicted correctly. To test these observations with another group of large RNAs, we have analyzed 15 ribosomal RNAs. Published secondary structure models that were derived by comparative sequence analysis were used to evaluate the predicted structures. Both the optimal predicted fold and the predicted "energy Dot Plot" of each sequence were examined. Each prediction was obtained from a single computer run on an entire ribosomal RNA sequence. All predicted base pairs in optimal foldings were examined for agreement with proven base pairs in the comparative models. Our analyses show that the overall correspondence between the predicted and comparative models varied for different RNAs and ranges from a low of 27% to high of 70%, with a mean value of 49%. The correspondence improves to a mean value of 81% when the analysis is limited to well-determined helices. In addition to well-determined helices, large well-determined structural domains can be observed in "energy Dot Plots" of some 16S ribosomal RNAs. The predicted domains correspond closely with structural domains that are found by the comparative method in the same RNAs. Our analyses also show that measuring the agreement between predicted and comparative secondary structure models underestimates the reliability of structural prediction by mfold.

  • Structural analysis by energy Dot Plot of a large mRNA
    Journal of Molecular Biology, 1993
    Co-Authors: Ann B. Jacobson, Michael Zuker
    Abstract:

    We have predicted the secondary structure of the entire 4217 nucleotide sequence of the genomic RNA of coliphage Q beta in one computer run using the computer program MFOLD that computes RNA structures within any prescribed increment of the computed minimum free energy. The results are presented in the form of an "energy Dot Plot" that shows both an optimal folding as well as the superposition of all base-pairs that can form in slightly suboptimal foldings. The Plot reveals five large, well-determined, independent structural domains that cover approximately 50% of the viral genome. The predicted structural domains are consistent with and provide support for five large structural domains identified previously by quantitative electron microscopy in Q beta RNA. The Dot Plot also contains cluttered regions that indicate large numbers of alternative foldings within or between segments of an RNA molecule. These reflect the impossibility of accurate structure prediction and/or the biological reality of more than one folding. Weaker, long range structures, that are observed by electron microscopy in two alternate competing conformations, are located in the regions of the Q beta sequence that correspond to cluttered regions of the Dot Plot. The potential biological significance of these secondary structures is discussed.

Michael Zuker - One of the best experts on this subject based on the ideXlab platform.

  • ‘Well-determined’ regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA
    Nucleic Acids Research, 1995
    Co-Authors: Michael Zuker, Ann B. Jacobson
    Abstract:

    Recent structural analyses of genomic RNAs from RNA coliphages suggest that both well-determined base paired helices and well-determined structural domains that are identified by "energy Dot Plot" analysis using the RNA folding package mfold, are likely to be predicted correctly. To test these observations with another group of large RNAs, we have analyzed 15 ribosomal RNAs. Published secondary structure models that were derived by comparative sequence analysis were used to evaluate the predicted structures. Both the optimal predicted fold and the predicted "energy Dot Plot" of each sequence were examined. Each prediction was obtained from a single computer run on an entire ribosomal RNA sequence. All predicted base pairs in optimal foldings were examined for agreement with proven base pairs in the comparative models. Our analyses show that the overall correspondence between the predicted and comparative models varied for different RNAs and ranges from a low of 27% to high of 70%, with a mean value of 49%. The correspondence improves to a mean value of 81% when the analysis is limited to well-determined helices. In addition to well-determined helices, large well-determined structural domains can be observed in "energy Dot Plots" of some 16S ribosomal RNAs. The predicted domains correspond closely with structural domains that are found by the comparative method in the same RNAs. Our analyses also show that measuring the agreement between predicted and comparative secondary structure models underestimates the reliability of structural prediction by mfold.

  • Structural analysis by energy Dot Plot of a large mRNA
    Journal of Molecular Biology, 1993
    Co-Authors: Ann B. Jacobson, Michael Zuker
    Abstract:

    We have predicted the secondary structure of the entire 4217 nucleotide sequence of the genomic RNA of coliphage Q beta in one computer run using the computer program MFOLD that computes RNA structures within any prescribed increment of the computed minimum free energy. The results are presented in the form of an "energy Dot Plot" that shows both an optimal folding as well as the superposition of all base-pairs that can form in slightly suboptimal foldings. The Plot reveals five large, well-determined, independent structural domains that cover approximately 50% of the viral genome. The predicted structural domains are consistent with and provide support for five large structural domains identified previously by quantitative electron microscopy in Q beta RNA. The Dot Plot also contains cluttered regions that indicate large numbers of alternative foldings within or between segments of an RNA molecule. These reflect the impossibility of accurate structure prediction and/or the biological reality of more than one folding. Weaker, long range structures, that are observed by electron microscopy in two alternate competing conformations, are located in the regions of the Q beta sequence that correspond to cluttered regions of the Dot Plot. The potential biological significance of these secondary structures is discussed.

Christophe Klopp - One of the best experts on this subject based on the ideXlab platform.

  • D-GENIES: Dot Plot large genomes in an interactive, efficient and simple way.
    PeerJ, 2018
    Co-Authors: Floréal Cabanettes, Christophe Klopp
    Abstract:

    Dot Plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment Dot Plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive Dot Plots. It enables users to sort query sequences along the reference, zoom in the Plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

Petre G. Pop - One of the best experts on this subject based on the ideXlab platform.

  • in memory dedicated Dot Plot analysis for dna repeats detection
    International Conference on Intelligent Computer Communication and Processing, 2016
    Co-Authors: Petre G. Pop
    Abstract:

    DNA repeats are believed to play significant roles in genome evolution and manifestation of severe diseases. Many of the methods for finding repeated sequences use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using DNA distances and consensus types) and an in-memory Dot-Plot analysis combined with image processing techniques, to visual isolate the positions of DNA repeats with different lengths.

  • ICCP - In-memory dedicated Dot-Plot analysis for DNA repeats detection
    2016 IEEE 12th International Conference on Intelligent Computer Communication and Processing (ICCP), 2016
    Co-Authors: Petre G. Pop
    Abstract:

    DNA repeats are believed to play significant roles in genome evolution and manifestation of severe diseases. Many of the methods for finding repeated sequences use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using DNA distances and consensus types) and an in-memory Dot-Plot analysis combined with image processing techniques, to visual isolate the positions of DNA repeats with different lengths.

  • dna repeats detection using a dedicated Dot Plot analysis
    International Conference on Telecommunications, 2015
    Co-Authors: Petre G. Pop
    Abstract:

    DNA repeats are believed to play significant roles in genome evolution and diseases. Many of the methods for finding repeated sequences are part of the digital signal processing (DSP) field and most of these methods use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using DNA distances and consensus types) and a custom Dot-Plot analysis (using similarities to represent DNA patterns) combined with image processing techniques, to isolate the position of DNA patterns with different lengths.

  • TSP - DNA repeats detection using a dedicated Dot-Plot analysis
    2015 38th International Conference on Telecommunications and Signal Processing (TSP), 2015
    Co-Authors: Petre G. Pop
    Abstract:

    DNA repeats are believed to play significant roles in genome evolution and diseases. Many of the methods for finding repeated sequences are part of the digital signal processing (DSP) field and most of these methods use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using DNA distances and consensus types) and a custom Dot-Plot analysis (using similarities to represent DNA patterns) combined with image processing techniques, to isolate the position of DNA patterns with different lengths.

  • DNA Patterns Localization Using a Dedicated Dot-Plot and Image Analysis
    2015
    Co-Authors: Petre G. Pop
    Abstract:

    DNA repeats are believed to play significant roles in genome evolution and diseases. Many of the methods for finding repeated sequences are part of the digital signal processing (DSP) field and most of these methods use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using DNA distances and consensus types) and a custom Dot-Plot analysis (using similarities to represent DNA patterns) combined with image processing techniques, to visual isolate the position of DNA patterns with different lengths. The final images that best put in evidence the presence of repeated sequences were obtained using weighted cosine cross-correlation, Jukes-Cantor distance and Motyka similarity.

N. Vries - One of the best experts on this subject based on the ideXlab platform.