Former Post Doc - Dr. rer. nat. - Kenneth W Berendzen : Scripts and Programs
Former Post-doctoral researcher: |  |
Motif Mapper
I am the principle creator and developer of Motif Mapper, a collection of (visual basic, .NET, python) scripts for various word counting tasks. As I have moved to the University of Tübingen, I am continuing my page-caring from here. Although there have been significant changes in the programming structure of the package, all basic principles and routines have remained the same. You are invited to view the description of the 3.1.2 release and enjoy the recent releases from here. All scripts are Open Source (GPL2) along with a Creative License (see below). GenBank extraction is best performed using the python version or the VBA versions. I have also included a simple GFF parser in the .NET version. All software is provided as is with no guuarentees. Comments are welcome.
Motif Mapper releases:
- documentation based on 3.1.2 release
- history VB
- python version
- license
- .NET version (see below)
VBA Scripts
- VBA installation options
- 3.3.2 (for TAIR v4.0)
- 3.4.0 (for TAIR v4.0, 5.0)
- 3.4.1 (for TAIR v4.0, 5.0)
- 3.5.0 (for TAIR v4.0, 5.0)
- 3.6.0 (for TAIR v7.0 and below)
- 4.0.1 (for TAIR v7.0 and below)
.NET(with VB2007)
- 5.2.4.01 (.NET version with full GUI interface, GFF promoter parser, Significant Motifs in Promoters)
Python
- description and history (GenBank promoter parser)
- win32 binary (most recent version)
- python sdist (most recent version)
Finding Significant Motifs In Promoters using the 'Cluster Analysis Real Randomization' algorithm
Use this program to identify significantly enriched or depleted motifs compared to a dynamically randomized background dataset. This program requires only FASTA formatted files for .NET versions or GenBank flat-files for the VB versions as input. A help - walk-through for the .NET version is provided. All other scripts are more or less the same as the 3.1.2 release (see above).
Motif Mapper scripts have been used/mentioned in several publications:
- Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription. Berendzen KW, Weiste C, Wanke D, Kilian J, Harter K, Dröge-Laser W. BMC Plant Biol. 2012 Aug 1;12:125.
Analysis of plant regulatory DNA sequences by transient protoplast assays and computer aided sequence evaluation. In: Methods in Molecular Biology: Plant Signal Transduction (Humana Press), accepted. Berendzen, K.W., Harter, K., Wanke, D. (2007).
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves . Kenneth W Berendzen , Kurt Stueber , Klaus Harter and Dierk Wanke. BMC Bioinformatics 2006, 7:522 doi:10.1186/1471-2105-7-522.
The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Santi L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C, Muller K, Muller J, Rohde W, Salamini F; Plant J. 2003 Jun;34(6):813-26.
Other Programs (a.k.a Motif Mapper add ons)
Protein-Protein Interaction Mining
Use this script to identify Protein-Protein interactions from specific binary datasets. This script is designed for mining public protein-protein network information, such as available from public databases TAIR's database found at TAIR's Proteome Resources - Protein-Protein Interactions.
Microarray Tools (Gene Sets)
Use these scripts for analyzing large collections of gene lists which may have partial or heavy redundancy. We have designed them to help us analyze the large number of gene sets we obtain when working with AtGenExpress data.
- UPDOWN overlap between many datasets
- Calculation of overlap between Gene lists, ListDistance. GUI version in 5.1.1.39 (see above).
Please contact me if you have any questions, comments, or suggestions. All scripts are Open Source and are released as additions (add ons) to the Motif Mapper package.
(c) KW. Berendzen, Uni-Tuebingen, ZMBP