SPIRE - Search for Prokaryotic Iron Response Elements

Downloading SPIRE

The most recent version of SPIRE can be found on GitHub at https://github.com/kblin/spire.

Running SIPRE

SPIRE depends on the excellent BioPython library, and the bioinf-helperlibs helper library.

If you install the two dependencies, you should be able to run spire from the directory it is located in.

./spire example.gbk

Run without any additional arguments, spire will print out diagnostics on how many IRE sequences were found. Calling spire with --help will show the additional output options. --text will show a human-readable overview of the results, --stats will show some statistics. Multiple output options can be used together.

License

SPIRE is licensed under the GNU General Public License version 3 or later, see the LICENSE file for details.

Citing SPIRE

If you found SPIRE useful, please cite The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494 Ewelina Michta, Klaus Schad, Kai Blin, Regina Ort-Winklbauer, Marc Röttig, Oliver Kohlbacher, Wolfgang Wohlleben, Eva Schinko, and Yvonne Mast Environmental Microbiology (2012) doi: 10.1111/1462-2920.12006