Newer version of AGEnt is available here: http://spineagent.fsm.northwestern.edu/cgi-bin/agent.cgi

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 provided

Core genome sequence(s) must be given in fasta or multi-fasta format (Example). Query genomic sequence(s) can be given in fasta or genbank (Example) format. A list of accessory genes will only be output if all sequences input are 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 optionally 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).

    • Gene coordinate information is NOT required for AGE-nt.

    Upload file size limit is 20 Mb.

    Core Genome Sequence:



    Query Genome Sequence:

    File type: ID:
    OPTIONAL: Query Genome Gene Coordinates: File format:

    Options:

    Minimum output sequence size, in bases.
    Miniumum overlap with accessory coordinates, in percent, for a gene to be called "accessory".
    Minimum nucmer alignment identity, in percent.


    Email Egon with questions or bugs.