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11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting PANGENOMICS: PERSISTENT HOMOLOGY FOR PAN-GENOME ANALYSIS Wednesday, 1st June 20:00 La Fonda NM Room (1st floor) Poster (PS‐1b.15) Alan Cleary 1 , Thiruvarangan Ramaraj 2 , Joann Mudge 2 , Brendan Mumey 1 1 Montana State University, 2 National Center for Genome Resources (NCGR) The sequencing of multiple accessions per species has brought an opportunity for doing pan‐genomic analyses, which can interrogate the unity and diversity within a species from a much broader perspective than looking at a single reference accession. Graph‐based pan‐genomic approaches have proven valuable but are subject to noise from artifacts which can change with parameters. True biological signal, however, will be more robust to changing parameters. In this work, we use persistent homology to quantify the significance of different features in pan‐genomes, revealing true biological signal including evolutionary relationships and guiding further investigation. Persistent homology is a method for computing topological features of a space at different spatial resolutions. More persistent features are detected over a wide range of resolutions and so are deemed more likely to represent true features of the underlying space. Since pan‐genomes can be represented at the nucleotide resolution as de Bruijn graphs, we treat k‐mer size as the spatial resolution. The features we track the persistence of are “bubbles” in the graph, which may represent heterozygous or homozygous variations, indels, repeats, or polymorphic sites, among other things. By varying the k‐mer size, we find which bubbles persist the longest within and among genomes. These data can be used to quantify the stability and significance of the features represented by the bubbles and can also define distance between different genomes within the population. Additionally, these data can be used to characterize interesting portions of the pan‐genome when sketching a representative visualization, as the graph is typically too dense to draw verbatim. Persistent homology helps to get beyond the noise in the data to identify true branch points in the data, thereby characterizing repeats, identifying more accurate relationships between accessions, pinpointing regions of the genome where distances between accessions differ from general trends (possibly indicating regions of local adaptation), and, conversely, establishing regions of the genome which are syntenic. 81
11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting USING MOLECULAR MODELS AND SEQUENCES TO UNDERSTAND NEW TECHNOLOGIES: CRISPR/CAS9 IN MOLECULE WORLD Wednesday, 1st June 20:00 La Fonda NM Room (1st floor) Poster (PS‐1b.16) Todd Smith, Sandra Porter Digital World Biology CRISPR/Cas9 is a hot topic. CRISPR/Cas9 is not only revolutionizing the field of gene editing, aspects of this system can be used to teach fundamental concepts in immunology and evolution. In terms of immunology, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and restriction/methylation systems protect bacteria from phage. CRISPR sequences are in essence an adaptive immune system for prokaryotes, storing information from previously encountered invaders. Molecular models provide insights in the following ways. Models illustrate the interaction between CRISPR DNA and viral RNA sequences. They show how Cas9 and related proteins can form complexes to cleave viral RNA. Further, as these systems are widespread in bacteria, models can be used to predict and discover new syste The excitement (and controversy) around CRISPR/Cas9 makes it a useful example for the classroom. Yet, there is a gap between this cutting edge research and educational use. Basic concepts about immunology, evolution, and inheritance of genetic information can be taught. For example, molecular models and sequence comparisons provide hands on ways for students to explore Cas9‐related protein structures from bacteria to learn about differences between homology and convergent evolution. To facilitate classroom use, we have created a collection of CRISPR/Cas9 and related structures and have made this freely available at www.digitalworldbiology.com/dwb/structure‐collections. This collection has been met with enthusiasm by biotechnology education programs (e.g. Madison College, WI) that incorporate CRISPR/Cas9 technologies in their curriculum. 82
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Reliable solutions for focused NGS
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