UPDATED:
  • Can upload multiple files for a single genome, as in the case of a multi-chromosome organism or chromsome + plasmids
  • Can now accept gff3-formatted annotation files with fasta sequence files
  • Performance improvements

    • Spine identifies a core genome from input genomic sequences. Sequences are aligned using Nucmer and regions found to be in common between all or a user-defined subset of genomes will be returned. Sequences can be given in fasta (Example), genbank (Example), or gff3 (Example) format. Annotation files in gff3 format must be accompanied by a separate sequence file in fasta format. Core and accessory genes will be output for any sequences given in annotated genbank format with locus_tag tags for each CDS or gff3 files including CDS records that are uploaded with fasta sequence files.

    Please enter only one genome per line. Records in multi-fasta files will be assumed to belong to the same genome (i.e. draft genomes consisting of scaffolds or contigs).

    Limit 2 - 15 genomes per analysis. Maximum of 20 Mb total file(s) size per genome. If analysis of a larger number of genomes or longer genomes is desired, please download the perl scripts to run locally (Link).

    IMPORTANT: Please note that the order in which genomes are entered may be important. Genomes entered first will be given highest priority in producing core genome sequence, with decreasing priority for each subsequently entered genome.


    Genome Sequences:

    Tip: Files can be dragged and dropped (in most browsers).
    Tip:Multiple files can be added for each genome (i.e. separate chromosomes or plasmids). Select multiple files to drag and drop onto the "Choose File" button or click the button and command- or control- click multiple files in the file-chooser window to upload.

    Genome #01: File type: Genome ID:
    Genome #02: File type: Genome ID:
    Genome #03: File type: Genome ID:
    Genome #04: File type: Genome ID:
    Genome #05: File type: Genome ID:
    Genome #06: File type: Genome ID:
    Genome #07: File type: Genome ID:
    Genome #08: File type: Genome ID:
    Genome #09: File type: Genome ID:
    Genome #10: File type: Genome ID:
    Genome #11: File type: Genome ID:
    Genome #12: File type: Genome ID:
    Genome #13: File type: Genome ID:
    Genome #14: File type: Genome ID:
    Genome #15: File type: Genome ID:

    Options:

    Minimum percent of all input genomes in which sequence must be present to be considered "core."
    Minimum percent identity of nucmer alignments to be considered homologous.
    Minimum core genome segment size to output, in bases.
    Maximum distance between core genome segments. Distances less than this between adjacent segments will result in combination of fragments with N's rather than separating into two or more fragments.
    Output pangenome


    Please wait for sequences to upload after pushing the button. Depending on your connection and genome sizes, this may take a few minutes

    Email Egon with questions or bugs.