AGEnt performs in silico subtractive hybridization of core genome sequences, such as those produced by Spine, against a query genomic sequence to identify accessory genomic sequences (AGEs) in the query genome. Sequences are aligned using Nucmer, outputting sequences and sequence characteristics of those regions in the query genome that are not found in the core genome. If gene coordinate information is provided, a list of accessory genes in the query genome will also be output.

Both the core genome sequence(s) and the query genome sequence(s) can be given in fasta (example) or genbank (example) format. A list of accessory genes will only be output if query sequence is in annotated genbank format with locus_tag tags for each CDS.

Gene information will be taken from the query file, if provided in Genbank format. If query sequence is given in fasta format, a list of gene coordinates may be separately provided in one of the following formats:

  • Glimmer format (Example). AGE-nt only uses the first three columns (gene id, start coordinate, stop coordinate).
  • GeneMark format (Example). Use the web output as a text file or the .lst file output by the downloaded version.
  • Prodigal format (Example from web version, Example from downloadable version).
  • GFF/GFF3 format (Example).

    Gene coordinate information is OPTIONAL for AGEnt.

    Total upload file size limit is 30 Mb.

    Tip: Files can be dragged and dropped (in most browsers)

    Core Genome Sequence:

    File type:

    Query Genome Sequence(s):

    Genomes spread across multiple files (i.e. chromsomes, plasmids) can be uploaded simultaneously by control- or command-clicking files in the file selection popup or dragging multiple files onto the buttons. All must be the same data type (all fasta or all genbank). File order is not important.

    File type: ID:
    OPTIONAL: Query Genome Gene Coordinate File(s): File format:

    Options:

    Minimum output sequence size, in bases.
    Minimum nucmer alignment identity, in percent.
    Output query core genome sequence (can be slow).


    Email Egon with questions or bugs.