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    • Latest Articles
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  • Types of Resources
    • Amplicon Sequence Collections
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Databases and Software

  • Open Access
    An Improved <span class="named-content genus-species" id="named-content-1">Caulobacter crescentus</span> Operon Annotation Based on Transcriptome Data
    Databases and Software
    An Improved Caulobacter crescentus Operon Annotation Based on Transcriptome Data

    Caulobacter crescentus is a model alphaproteobacterium with a well-studied genetic network controlling its cell cycle. Essential for such studies is an accurate map of the expressed features of its genome. Here, we provide an updated map of the expressed RNAs by integrative analysis of 5′ global rapid amplification of cDNA ends, transcriptome sequencing, rifampicin...

    Mohammed-Husain Bharmal, James R. Aretakis, Jared M. Schrader
  • Open Access
    COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database
    Databases and Software
    COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database

    We introduce COnTORT (COmprehensive Transcriptomic ORganizational Tool), a publicly available program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream...

    Kevin S. Myers, Michael Place, Daniel R. Noguera, Timothy J. Donohue
  • Open Access
    GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining
    Databases and Software
    GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining

    Amplicon sequencing of the 16S rRNA gene is commonly performed for the assessment and comparison of microbiomes. Here, we introduce GenePiper, an open-source R Shiny application that provides an easy-to-use interface, a wide range of analytical methods, and optimized graphical outputs for offline microbiome data analyses.

    W. M. Tong, Yuki Chan
  • Open Access
    TwinBLAST: When Two Is Better than One
    Databases and Software
    TwinBLAST: When Two Is Better than One

    Analysis of sequence read pairs can be essential for characterizing structural variation, including junction-spanning pairs of reads (JSPRs) suggesting recent lateral/horizontal gene transfer. TwinBLAST can be used to facilitate this analysis of JSPRs by enabling the visualization and curation of two BLAST reports side by side in a single interface.

    Julie C. Dunning Hotopp, James Matsumura, Robin E. Bromley, David R. Riley, Sonia Agrawal, Ben Sparklin, John Mattick, Jonathan Crabtree, Anup Mahurkar
  • Open Access
    gndDb, a Database of Partial <em>gnd</em> Sequences To Assist with Analysis of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Communities Using High-Throughput Sequencing
    Databases and Software
    gndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing

    The use of culture methods to detect Escherichia coli diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target the hypervariable gnd gene and describe a database containing 534 distinct partial gnd sequences and associated O groups for use with culture-independent...

    Adrian L. Cookson, David W. Lacher, Flemming Scheutz, David A. Wilkinson, Patrick J. Biggs, Jonathan C. Marshall, Gale Brightwell
  • Open Access
    T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees
    Databases and Software
    T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees

    The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.

    Ignazio Carbone, James B. White, Jolanta Miadlikowska, A. Elizabeth Arnold, Mark A. Miller, Nicolas Magain, Jana M. U'Ren, François Lutzoni
  • Open Access
    omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection
    Databases and Software
    omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection

    Metabolomics is a powerful tool for measuring the functional output of the microbiota. Currently, there are few established workflows for analysis downstream of metabolite identification.

    Connor R. Tiffany, Andreas J. Bäumler
  • Open Access
    A Curated, Comprehensive Database of Plasmid Sequences
    Databases and Software
    A Curated, Comprehensive Database of Plasmid Sequences

    Plasmid sequences are central to a myriad of microbial functions and processes. Here, we have compiled a database of complete plasmid sequences and associated metadata curated from both NCBI’s recent genome database update, which includes plasmids as organisms, and all available annotated bacterial genomes.

    Lauren Brooks, Mo Kaze, Mark Sistrom
  • Open Access
    ZetaHunter, a Reproducible Taxonomic Classification Tool for Tracking the Ecology of the <em>Zetaproteobacteria</em> and Other Poorly Resolved Taxa
    Databases and Software
    ZetaHunter, a Reproducible Taxonomic Classification Tool for Tracking the Ecology of the Zetaproteobacteria and Other Poorly Resolved Taxa
    Sean M. McAllister, Ryan M. Moore, Clara S. Chan
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