Results for "Genome"

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  • A quick #guide for student-driven community #genome #annotation https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006682

    Tags: guide, genome, annotation

    1817 days ago

  • CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

    Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975

    Tags: CAUSEL, epigenome, genome, editing, pipeline, function, noncoding, GWAS, variants

    1816 days ago

  • GMASS: a novel measure for genomeassembly structural similarity

    The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-z

    Tags: GMASS, novel, measure, genome, assembly, structural, similarity

    1810 days ago

  • The Rogers Lab

    The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Dro...

    Tags: Rebekah, Rogers, evolution, genome, structure

    1719 days ago

  • Apollo: First instantaneous, collaborative genomic annotation editor available on the Web

    Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’. ...

    Tags: Apollo, collaborative, genomic, annotation, editor, Web, genome

    1764 days ago

  • Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

    Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.   Cogent is a tool for reconstruct...

    Tags: Cogent, tool, reconstruct, coding, genome, high-quality, full-length, transcriptome, sequences, genome, evaluation

    1746 days ago

  • Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

    Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAP

    Tags: Integrative, Meta-Assembly, Pipeline, IMAP, Chromosome-level, genome, assembler, multiple, de novo, assemblies

    1672 days ago

  • ALF--a simulation framework for genome evolution.

    Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article: Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimo...

    Tags: ALF, simulation, framework, genome, evolution

    1619 days ago

  • simuG: a general-purpose genome simulator

    Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy num...

    Tags: simuG, general-purpose, genome, simulator

    1583 days ago

  • 5700 year-old human genome !

    A Landmark in genomics, scientists have done something that hasn't been done ever. Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance. By sequencing the sample, researchers not onl...

    Tags: reconstructed, genome, human, 5700, years, Denmark, ancient

    1562 days ago