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Evolution 2012
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Kate Hertweck
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Hertweck and Pires presentation from Evolution 2012 in Ottawa, in the Genomics 7 session.
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Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output. This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
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CRISPR/Cas9 gene editing is based on a microbial restriction system, that has been harnessed for genome targeting using only a short sequence of RNA as a guide. The beauty of the system is that unlike protein binding based technologies such as Zinc Fingers and TALENs which require complex protein engineering, the design rules are very simple, and it is this fact that is allowing CRISPR to take genome engineering from a relatively niche persuit to the mainstream scientific community. The principle of the system is that a short guide RNA, homologous to the target site recruits a nuclease – Cas9 This then cuts the dsDNA, triggering repair by either the low fidelity NHEJ pathway, or by HDR in the presence of an exogenous donor sequence. High Efficiencies for both knockouts and knock-ins have been reported and whilst there are understandable concerns about specificity, new methodologies to address these are now being developed The system itself is comprised of three key components the Cas9 protein, which cuts/cleaves the DNA and Two RNAs - a crispr RNA contains the sequence homologous to the target site and a trans-activating crisprRNA (or TracrRNA) which recruits the nuclease/crispr complex For genome editing, the crisperRNA and TraceRNA are generally now constructed together into a single guideRNA or sgRNA Genome editing is elicited through hybridization of the sgRNA with its matching genomic sequence, and the recruitment of the Cas9, which cleaves at the target site.
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Recommandé
useR2011 - Huber
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An update version of the genome assembly including the mention of techniques such as HiC and Bionano. Also include the QC. These are the same slides used in the course for the UNL in Argentina.
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Kogo 2013 RNA-seq analysis
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Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output. This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
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Golden Helix Inc
CRISPR-cas9 system is a new robust genome editing tool and also this is a really easy to use system. کاربرد سیستم کریسپر در ویرایش ژنوم.ppt
the application of CRISPR/Cas9 system in genome editing
the application of CRISPR/Cas9 system in genome editing
Arash zolnori
CRISPR/Cas9 gene editing is based on a microbial restriction system, that has been harnessed for genome targeting using only a short sequence of RNA as a guide. The beauty of the system is that unlike protein binding based technologies such as Zinc Fingers and TALENs which require complex protein engineering, the design rules are very simple, and it is this fact that is allowing CRISPR to take genome engineering from a relatively niche persuit to the mainstream scientific community. The principle of the system is that a short guide RNA, homologous to the target site recruits a nuclease – Cas9 This then cuts the dsDNA, triggering repair by either the low fidelity NHEJ pathway, or by HDR in the presence of an exogenous donor sequence. High Efficiencies for both knockouts and knock-ins have been reported and whilst there are understandable concerns about specificity, new methodologies to address these are now being developed The system itself is comprised of three key components the Cas9 protein, which cuts/cleaves the DNA and Two RNAs - a crispr RNA contains the sequence homologous to the target site and a trans-activating crisprRNA (or TracrRNA) which recruits the nuclease/crispr complex For genome editing, the crisperRNA and TraceRNA are generally now constructed together into a single guideRNA or sgRNA Genome editing is elicited through hybridization of the sgRNA with its matching genomic sequence, and the recruitment of the Cas9, which cleaves at the target site.
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Presented at Plant Genomics and Gene Editing Congress: Europe. For more information visit: www.global-engage.com In a context of climate change and limited energy resources, better understanding of how plants evolve and adapt is a major goal. However, despite the revolution of the NGS technologies, the study of plant genomes remains challenging due to their size, polyploidy and high percentage of repetitive elements.
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