GenomeDiagram is a Python module for drawing publication-quality images (circular and linear diagrams) of genome sequences and data at arbitrary scales (up to A0 and beyond). GenomeDiagram can take whole genome files and arbitrary data as input, displaying them on individual (or combined) tracks. The package can draw graphs of arbitrary data values, and is highly customisable. GenomeDiagram is co-authored by Leighton Pritchard and Jennifer White.

GenomeDiagram was announced in:

• Pritchard et al. (2006), Bioinformatics 22 616-617

has been used in the following publications:

• Toth et al. (2006), Ann. Rev. Phytopath. 44 305-336
• Bell et al. (2004), Proc. Natl. Acad. Sci. USA 101 11105-11110

and is the subject of an artistic collaboration between Ian Toth, Elaine Shemilt, Michel Perombelon, Genevieve Murphy, Paul Harrison, Danny Hill and Leighton Pritchard.

GenomeDiagram is written in Python and available as a module, and as a standalone Windows application. To use the GUI from source, wxPython, ReportLab and BioPython are required.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should receive a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

For reference, you can find a copy of the GNU General Public License at http://www.gnu.org/licenses/gpl.txt.

A Python wrapper for the Zerg BLAST parser, with build instructions
Requires Zerg and Python to be correctly locally installed to use the libraries. Also, Pyrex is required to build the wrapper from the supplied files.
The Zerg parser is described in Paquola et al (2003), Bioinformatics 19, 1035-1036, and its home page is located at http://bioinfo.iq.usp.br/zerg/

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should receive a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

For reference, you can find a copy of the GNU General Public License at http://www.gnu.org/licenses/gpl.txt.

FindSeq is a Python module for finding nucleotide sequence motifs in a larger nucleotide sequence. It can be used to identify individual motifs, or pairs of motifs separated by an arbitrary distance (with both upper and lower bounds).

Findseq has been used in the following publications:

• Whisson et al. (2005) Fungal Genetics and Biology 42 351-365

FindSeq is written in Python and available as a module. It requires BioPython to run from source.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should receive a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

For reference, you can find a copy of the GNU General Public License at http://www.gnu.org/licenses/gpl.txt.

Choosing 'random' wells from a plate is prone to the same problems as choosing 'random' lottery numbers. The natural human tendency is to pick well-spaced, nonrandom wells. The program Wellpicker makes a (pseudo)random choice of wells from an arbitrary number of plates of arbitrary size.

Wellpicker is written in Python and available as standalone Windows and OS X packages. To run from source, wxPython is required.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should receive a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

For reference, you can find a copy of the GNU General Public License at http://www.gnu.org/licenses/gpl.txt