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annotation

  • Open Access
    Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
    Research Article | Host-Microbe Biology
    Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

    It is now relatively easy to obtain a high-quality draft genome sequence of a bacterium, but bioinformatic analysis requires organization and optimization of multiple open source software tools. We present Bactopia, a pipeline for bacterial genome analysis, as an option for processing bacterial genome data. Bactopia also automates downloading of data from multiple public sources and species-specific customization. Because the pipeline...

    Robert A. Petit, Timothy D. Read
  • Open Access
    Curated BLAST for Genomes
    Methods and Protocols | Novel Systems Biology Techniques
    Curated BLAST for Genomes

    Given a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without...

    Morgan N. Price, Adam P. Arkin
  • Open Access
    PaperBLAST: Text Mining Papers for Information about Homologs
    Methods and Protocols | Novel Systems Biology Techniques
    PaperBLAST: Text Mining Papers for Information about Homologs

    With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about...

    Morgan N. Price, Adam P. Arkin
  • Open Access
    RNA Sequencing-Based Genome Reannotation of the Dermatophyte <em>Arthroderma benhamiae</em> and Characterization of Its Secretome and Whole Gene Expression Profile during Infection
    Research Article | Host-Microbe Biology
    RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection
    Van Du T. Tran, Niccolò De Coi, Marc Feuermann, Emanuel Schmid-Siegert, Elena-Tatiana Băguţ, Bernard Mignon, Patrice Waridel, Corinne Peter, Sylvain Pradervand, Marco Pagni, Michel Monod
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