The Experts below are selected from a list of 5274 Experts worldwide ranked by ideXlab platform

Benjamin M Peter - One of the best experts on this subject based on the ideXlab platform.

  • authentict a model of ancient dna damage to estimate the proportion of present day dna contamination
    Genome Biology, 2020
    Co-Authors: Stephane Peyregne, Benjamin M Peter
    Abstract:

    Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a Command-Line Tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.

  • authentict a model of ancient dna damage to estimate the proportion of present day dna contamination
    bioRxiv, 2020
    Co-Authors: Stephane Peyregne, Benjamin M Peter
    Abstract:

    ABSTRACT Summary Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a Command-Line Tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available. Contact stephane.peyregne@gmail.com

Martin Kollmar - One of the best experts on this subject based on the ideXlab platform.

  • waggawagga cli a Command Line Tool for predicting stable single α helices sah domains and the sah domain distribution across eukaryotes
    PLOS ONE, 2018
    Co-Authors: Dominic Simm, Martin Kollmar
    Abstract:

    Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a Command-Line Tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses.

  • SAH-domain analysis of eukaryotic genomes
    2018
    Co-Authors: Martin Kollmar, Dominic Simm
    Abstract:

    These files contain the Supplementary data for the the study "Waggawagga-CLI: A Command-Line Tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes

Jay Shendure - One of the best experts on this subject based on the ideXlab platform.

  • flashfry a fast and flexible Tool for large scale crispr target design
    BMC Biology, 2018
    Co-Authors: Aaron Mckenna, Jay Shendure
    Abstract:

    Genome-wide knockout studies, noncoding deletion scans, and other large-scale studies require a simple and lightweight framework that can quickly discover and score thousands of candidate CRISPR guides targeting an arbitrary DNA sequence. While several CRISPR web applications exist, there is a need for a high-throughput Tool to rapidly discover and process hundreds of thousands of CRISPR targets. Here, we introduce FlashFry, a fast and flexible Command-Line Tool for characterizing large numbers of CRISPR target sequences. With FlashFry, users can specify an unconstrained number of mismatches to putative off-targets, richly annotate discovered sites, and tag potential guides with commonly used on-target and off-target scoring metrics. FlashFry runs at speeds comparable to commonly used genome-wide sequence aligners, and output is provided as an easy-to-manipulate text file. FlashFry is a fast and convenient Command-Line Tool to discover and score CRISPR targets within large DNA sequences.

  • flashfry a fast and flexible Tool for large scale crispr target design
    bioRxiv, 2017
    Co-Authors: Aaron Mckenna, Jay Shendure
    Abstract:

    FlashFry is a fast and flexible Command-Line Tool for characterizing large numbers of CRISPR target sequences. While several CRISPR web application exist, genome-wide knockout studies, noncoding deletion scans, and other large-scale studies or methods development projects require a simple and lightweight framework that can quickly discover and score thousands of candidates guides targeting an arbitrary DNA sequence. With FlashFry, users can specify an unconstrained number of mismatches to putative off-targets, richly annotate discovered sites, and tag potential guides with commonly used on-target and off-target scoring metrics. FlashFry runs at speeds comparable to widely used genome-wide sequence aligners, and output is provided as an easy-to-manipulate text file.

Dominic Simm - One of the best experts on this subject based on the ideXlab platform.

  • waggawagga cli a Command Line Tool for predicting stable single α helices sah domains and the sah domain distribution across eukaryotes
    PLOS ONE, 2018
    Co-Authors: Dominic Simm, Martin Kollmar
    Abstract:

    Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a Command-Line Tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses.

  • SAH-domain analysis of eukaryotic genomes
    2018
    Co-Authors: Martin Kollmar, Dominic Simm
    Abstract:

    These files contain the Supplementary data for the the study "Waggawagga-CLI: A Command-Line Tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes

Stephane Peyregne - One of the best experts on this subject based on the ideXlab platform.

  • authentict a model of ancient dna damage to estimate the proportion of present day dna contamination
    Genome Biology, 2020
    Co-Authors: Stephane Peyregne, Benjamin M Peter
    Abstract:

    Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a Command-Line Tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.

  • authentict a model of ancient dna damage to estimate the proportion of present day dna contamination
    bioRxiv, 2020
    Co-Authors: Stephane Peyregne, Benjamin M Peter
    Abstract:

    ABSTRACT Summary Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a Command-Line Tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available. Contact stephane.peyregne@gmail.com