The Experts below are selected from a list of 327 Experts worldwide ranked by ideXlab platform

Jacques Van Helden - One of the best experts on this subject based on the ideXlab platform.

  • rsat 2011 Regulatory Sequence analysis tools
    Nucleic Acids Research, 2011
    Co-Authors: Morgane Thomaschollier, Olivier Sand, Matthieu Defrance, Alejandra Medinarivera, Carl Herrmann, Denis Thieffry, Jacques Van Helden
    Abstract:

    RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-Regulatory elements in genome Sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated Sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale Sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, Sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak Sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/.

  • rsat Regulatory Sequence analysis tools
    Nucleic Acids Research, 2008
    Co-Authors: Morgane Thomaschollier, Olivier Sand, Jean Valery Turatsinze, Rekins Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohee, Jacques Van Helden
    Abstract:

    The Regulatory Sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-Regulatory elements in genome Sequences. The suite includes programs for Sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random Sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.

  • Regulatory Sequence analysis tools
    Nucleic Acids Research, 2003
    Co-Authors: Jacques Van Helden
    Abstract:

    The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of Regulatory sites in non-coding DNA Sequences. These tools include Sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random Sequence generation and other utilities. Alternative formats are supported for the representation of Regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully Sequenced genomes and these data are regularly updated from GenBank.

David P Giedroc - One of the best experts on this subject based on the ideXlab platform.

  • functional transcriptional Regulatory Sequence trs rna binding and helix destabilizing determinants of murine hepatitis virus mhv nucleocapsid n protein
    Journal of Biological Chemistry, 2012
    Co-Authors: Sarah C Keane, Julian L Leibowitz, David P Giedroc
    Abstract:

    Abstract Coronavirus (CoV) nucleocapsid (N) protein contains two structurally independent RNA binding domains. These are denoted N-terminal domain (NTD) and C-terminal domain and are joined by a charged linker region rich in serine and arginine residues (SR linker). In mouse hepatitis virus (MHV), the NTD binds the transcriptional Regulatory Sequence (TRS) RNA, a conserved hexanucleotide Sequence required for subgenomic RNA synthesis. The NTD is also capable of disrupting a short RNA duplex. We show here that three residues on the β3 (Arg-125 and Tyr-127) and β5 (Tyr-190) strands play key roles in TRS RNA binding and helix destabilization with Ala substitutions of these residues lethal to the virus. NMR studies of the MHV NTD·TRS complex revealed that this region defines a major RNA binding interface in MHV with site-directed spin labeling studies consistent with a model in which the adenosine-rich 3′-region of TRS is anchored by Arg-125, Tyr-127, and Tyr-190 in a way that is critical for efficient subgenomic RNA synthesis in MHV. Characterization of CoV N NTDs from infectious bronchitis virus and from severe acute respiratory syndrome CoV revealed that, although detailed NTD-TRS determinants are distinct from those of MHV NTD, rapid helix destabilization activity of CoV N NTDs is most strongly correlated with CoV function and virus viability.

  • coronavirus n protein n terminal domain ntd specifically binds the transcriptional Regulatory Sequence trs and melts trs ctrs rna duplexes
    Journal of Molecular Biology, 2009
    Co-Authors: Nicholas E Grossoehme, Lichun Li, Sarah C Keane, Charles E Dann, Julian L Leibowitz, David P Giedroc
    Abstract:

    All coronaviruses (CoVs), including the causative agent of severe acute respiratory syndrome (SARS), encode a nucleocapsid (N) protein that harbors two independent RNA binding domains of known structure, but poorly characterized RNA binding properties. We show here that the N-terminal domain (NTD) of N protein from mouse hepatitis virus (MHV), a virus most closely related to SARS-CoV, employs aromatic amino acid-nucleobase stacking interactions with a triple adenosine motif to mediate high-affinity binding to single-stranded RNAs containing the transcriptional Regulatory Sequence (TRS) or its complement (cTRS). Stoichiometric NTD fully unwinds a TRS-cTRS duplex that mimics a transiently formed transcription intermediate in viral subgenomic RNA synthesis. Mutation of the solvent-exposed Y127, positioned on the β-platform surface of our 1.75 A structure, binds the TRS far less tightly and is severely crippled in its RNA unwinding activity. In contrast, the C-terminal domain (CTD) exhibits no RNA unwinding activity. Viruses harboring Y127A N mutation are strongly selected against and Y127A N does not support an accessory function in MHV replication. We propose that the helix melting activity of the coronavirus N protein NTD plays a critical accessory role in subgenomic RNA synthesis and other processes requiring RNA remodeling.

Sebastien Jaeger - One of the best experts on this subject based on the ideXlab platform.

  • rsat 2015 Regulatory Sequence analysis tools
    Nucleic Acids Research, 2015
    Co-Authors: Alejandra Medinarivera, Olivier Sand, Matthieu Defrance, Carl Herrmann, Jaime A Castromondragon, Jeremy Delerce, Sebastien Jaeger
    Abstract:

    RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-Regulatory elements in genome Sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of Regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract Sequences from a list of coordinates (fetch-Sequences from UCSC), novel programs dedicated to the analysis of Regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of Sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

Carl Herrmann - One of the best experts on this subject based on the ideXlab platform.

  • rsat 2015 Regulatory Sequence analysis tools
    Nucleic Acids Research, 2015
    Co-Authors: Alejandra Medinarivera, Olivier Sand, Matthieu Defrance, Carl Herrmann, Jaime A Castromondragon, Jeremy Delerce, Sebastien Jaeger
    Abstract:

    RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-Regulatory elements in genome Sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of Regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract Sequences from a list of coordinates (fetch-Sequences from UCSC), novel programs dedicated to the analysis of Regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of Sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

  • rsat 2011 Regulatory Sequence analysis tools
    Nucleic Acids Research, 2011
    Co-Authors: Morgane Thomaschollier, Olivier Sand, Matthieu Defrance, Alejandra Medinarivera, Carl Herrmann, Denis Thieffry, Jacques Van Helden
    Abstract:

    RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-Regulatory elements in genome Sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated Sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale Sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, Sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak Sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/.

Matthieu Defrance - One of the best experts on this subject based on the ideXlab platform.

  • rsat 2015 Regulatory Sequence analysis tools
    Nucleic Acids Research, 2015
    Co-Authors: Alejandra Medinarivera, Olivier Sand, Matthieu Defrance, Carl Herrmann, Jaime A Castromondragon, Jeremy Delerce, Sebastien Jaeger
    Abstract:

    RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-Regulatory elements in genome Sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of Regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract Sequences from a list of coordinates (fetch-Sequences from UCSC), novel programs dedicated to the analysis of Regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of Sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

  • rsat 2011 Regulatory Sequence analysis tools
    Nucleic Acids Research, 2011
    Co-Authors: Morgane Thomaschollier, Olivier Sand, Matthieu Defrance, Alejandra Medinarivera, Carl Herrmann, Denis Thieffry, Jacques Van Helden
    Abstract:

    RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-Regulatory elements in genome Sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated Sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale Sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, Sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak Sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/.

  • rsat Regulatory Sequence analysis tools
    Nucleic Acids Research, 2008
    Co-Authors: Morgane Thomaschollier, Olivier Sand, Jean Valery Turatsinze, Rekins Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohee, Jacques Van Helden
    Abstract:

    The Regulatory Sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-Regulatory elements in genome Sequences. The suite includes programs for Sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random Sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.