SPIRE

Search for Prokaryote Iron Response Elements

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.

Copyright 2008-2012 Kai Blin

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