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    Average Nucleotide Identity (ANI)

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    Neeraj
    Average Nucleotide Identity (ANI) is a measure of genomic similarity between two genomes that compares coding regions. ANI is computed by first finding bidirectional best hits (BBHs) between gene pairs that share at least 70% identity and 70% coverage. Alignment Fraction (AF) is also calculated using the proportion of bases aligned between the genomes. Pairwise ANI values are precomputed and displayed, while private or new genomes are computed on demand. Genomes can be analyzed and grouped based on their ANI and AF values within species or taxonomies. Clique groups represent strongly connected genome subgroups within a species. ANI information for individual genomes can also be found on their detail pages.

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    Average Nucleotide Identity (ANI)

    Uploaded by

    Neeraj
    68 views13 pages
    Average Nucleotide Identity (ANI) is a measure of genomic similarity between two genomes that compares coding regions. ANI is computed by first finding bidirectional best hits (BBHs) between gene pairs that share at least 70% identity and 70% coverage. Alignment Fraction (AF) is also calculated using the proportion of bases aligned between the genomes. Pairwise ANI values are precomputed and displayed, while private or new genomes are computed on demand. Genomes can be analyzed and grouped based on their ANI and AF values within species or taxonomies. Clique groups represent strongly connected genome subgroups within a species. ANI information for individual genomes can also be found on their detail pages.

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    ANI

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    Average Nucleotide Identity (ANI) is a measure of genomic similarity between two genomes that compares coding regions. ANI is computed by first finding bidirectional best hits (BBHs) between gene pairs that share at least 70% identity and 70% coverage. Alignment Fraction (AF) is also calculated using the proportion of bases aligned between the genomes. Pairwise ANI values are precomputed and displayed, while private or new genomes are computed on demand. Genomes can be analyzed and grouped based on their ANI and AF values within species or taxonomies. Clique groups represent strongly connected genome subgroups within a species. ANI information for individual genomes can also be found on their detail pages.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    68 views13 pages

    Average Nucleotide Identity (ANI)

    Uploaded by

    Neeraj
    Average Nucleotide Identity (ANI) is a measure of genomic similarity between two genomes that compares coding regions. ANI is computed by first finding bidirectional best hits (BBHs) between gene pairs that share at least 70% identity and 70% coverage. Alignment Fraction (AF) is also calculated using the proportion of bases aligned between the genomes. Pairwise ANI values are precomputed and displayed, while private or new genomes are computed on demand. Genomes can be analyzed and grouped based on their ANI and AF values within species or taxonomies. Clique groups represent strongly connected genome subgroups within a species. ANI information for individual genomes can also be found on their detail pages.

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    Average Nucleotide Identity (ANI)

    Introduction

    Average Nucleotide Identity (ANI) is a measure of nucleotide-level genomic similarity


    between the coding regions of two genomes. First, BBHs between a genome pair are
    computed as pairwise bidirectional best nSimScan hits of genes having 70% or more
    identity and at least 70% coverage of the shorter gene.

    Alignment Fraction (AF) is computed using to the following formula:

    Average Nucleotide Identity (ANI) is computed using the following formula:


    Pairwise ANI

    BBHs between a genome pair are computed as pairwise bidirectional best nSimScan
    hits of genes having 70% or more identity and at least 70% coverage of the shorter
    gene. Genome(s) can either be selected from IMG or uploaded as a nucleotide
    sequence in FASTA format (using the ​Upload File button) to compute ANI to selected
    genome(s) in IMG.

    Figure 1​. ANI Pairwise

    Pairwise ANI is precomputed for most genomes. Private genomes and newly added
    genomes will be precomputed on-demand which will slow down the computation (Fig.
    1b).
    Figure 1b​. Pairwise ANI - results
    Same Species Plot

    Figure 2​. Same Species Plot - Species table

    Selecting in the Species table under “Number of Genomes” for a species links to the
    “Genomes for Species” page (Fig. 2b). Selecting “Number of Cliques” for a species links
    to the “Cliques for Species” page (Fig. 2c).
    Figure 2b​. Genomes for Species

    Figure 2c​. Cliques for Species


    Figure 2d​. Same Species Plot

    Each dot in the Same Species Plot represents the final ANI vs. final AF for a genome
    pair present in a given species. Selecting a dot will bring up a dialog box with a table to
    which the 2 genomes represented in the dot will be added. These genomes can then be
    reviewed and added to a genome cart.
    ANI Cliques

    Figure 3​. ANI Cliques - by clique ID

    Clicking on the clique id in the All Cliques tab will link to the details page for that clique
    (Fig. 4).
    Figure 3b​. ANI Cliques by Species
    Figure 3c​. ANI Cliques by Taxonomy

    The leaf nodes in the Taxonomy tree display the ​Genus Species followed by the count
    of cliques for that genus-species. Clicking on the count links to the Genus Species detail
    page. The first tab of this page lists the cliques for this Species (Fig. 3d), while the
    second tab lists the genomes in that Species (Fig. 3f).
    Figure 3d​. Genus Species Detail page - Cliques for Species

    Figure 3f​. Genus Species Detail page - Genomes for Species


    Figure 3g​. ANI Cliques - Clique Groups

    Any two genomes in a clique group will be connected by an edge in the graph if they
    have an ANI >= 96.5 and an AF >= 0.6. Clicking on the clique graph representation links
    to details page for that clique group (Fig. 4).

    Clique Details

    Figure 4​. Clique Details - Overview


    Figure 4b​. Clique Details - Genomes in Clique

    Figure 4c​. Clique Details - Similar Cliques


    Figure 4d​. Clique Details - Clique Group

    Genome Detail Page

    ANI information for a particular genome can be found on the genome detail page,
    located to the right of Genome Statistics.

    Figure 5​. Genome Detail - ANI

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