Bioinformatic tools for comparative genomic analysis
Developed by Egon A. Ozer at the Alan R. Hauser lab at Northwestern University Feinberg School of Medicine.

If you find the tools Spine and AGEnt useful in your own research, please cite our manuscript:
Ozer EA, Allen JP, and Hauser AR. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. BMC Genomics 2014 15:737

If you use ClustAGE, please cite this manuscript:
Ozer EA. ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements. BMC Bioinformatics 2018 19:150

News

2-6-2018
  • Updated Spine and AGEnt to version 0.3.1. Both programs now can accept genomes divided across multiple sequence files (i.e. chromosomes, plasmids). Both Spine and AGEnt can now accept gff3 annotation files from the Ensembl database.
  • Updated ClustAGE to version 0.8. Speed and performance improvements as well as option for pdf graphical output.
  • Updated ClustAGE Plot to warn if accessory genome sizes exceed maximum allowable by CGView (20 Mb). Also produces pdf output for higher quality figures.

    • 9-22-2017
  • Updated both Spine and AGEnt to versions 0.2.2. Fixed small bugs in handling of contigs composed entirely of ambiguous bases and handling of annotations at contig ends.
  • Updated ClustAGE to version 0.7.7. Also added link to ClustAGE source code for download. See download page for link.

    • 11-29-2016
  • Updated Spine to version 0.2.1 and AGEnt to version 0.2.1. Fixed bugs in both where first coding sequence on a contig would not be output to _loci.txt files.

    • 9-23-2016
  • Added online version of ClustAGE, a tool for clustering and examining distributions of accessory elements among genomes.
  • Added ClustAGE Plot for visualization of accessory element distributions produced by ClustAGE.
  • Updated Spine to version 0.2. This new version outputs core and accessory sequence for all provided genomes, as well as determining core and accessory coding sequences for any genomes for which annotation information is provided. Added option to output pangenome sequence.
  • Updated AGEnt to version 0.2. Output core and accesory genome sequence for the provided query genome. Added GFF file support.
  • Will be moving downloadable versions of software to GitHub for improved tracking and version control.

    • 1-26-2015 Updates:
  • Upgraded both online and downloadable versions of AGEnt to version 0.1.3. The only change is a bug fix in the nucmer_difference script: contigs in the query sequence that aligned one or more times to the reference, but none of the alignment identities were above the given threshold, were erroneously excluded from the output accessory genome. This is unlikely to have been a common occurence when using the default setting of an 85% identity cutoff in the downloadable version, but may have made a significant impact for higher percent identity cutoffs with short query contigs. I would encourage re-checking previous AGEnt results using the newer version.
  • Fixed link to Downloads from Spine page (thanks DG).

    • 10-16-2014 Updates:
  • AGEnt now accepts ORF prediction coordinate files as output by Glimmer, GeneMarkS, or Prodigal.
  • Downloadable version of AGEnt now includes scripts to convert output of GeneMarkS or Prodigal ORF prediction software to Glimmer format for use in AGEnt.
  • Fixed bug in online and downloadable versions of Genbank Reformat resulting in some CDS records not being output. New version is 0.1.3

    • 9-10-2014 Updates:
  • Updated downloadable versions of Spine, AGEnt, and Genbank Reformat to versions 0.1.2. Added ability of the programs to accept files created on Unix/Linux, Mac, and DOS/Windows.

    • 9-8-2014 Updates:
  • Updated online versions of Spine and AGEnt to accept sequence and/or coordinate files created not only on Unix/Linux systems, but also files produced by DOS or MacOSX systems.

    • 6-13-2014 Updates:
  • Provided wrapper scripts for Spine and AGEnt in Downloads section to allow all steps of the processes to be run from a single script.

    • 4-21-2014 Updates:
  • Moved applications to permanent server
  • Added dynamically updating progress reports for SPINE and AGEnt runs
  • Added Genbank reformatter application to help format multi-sequence Genbank files for SPINE and AGEnt

    • 1-18-2014 Applications are live on temporary server. Will be migrated to new server (vfsmspineagent.fsm.northwestern.edu) in the near future.