Spine

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

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) or genbank (Example) format. Core and accessory genes will only be output if all sequences input are in annotated genbank format with locus_tag tags for each CDS and in a single molecule, i.e. no contigs.

Please enter only one genome per file. 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. If analysis of a larger number of 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 output sequence, with decreasing priority for each subsequently entered genome.

Genome Sequences:

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


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.