Berkeley Drosophila Transcription Network Project

The BDTNP has put together a variety of resources to assist in the processing and interpretation of Affymetrix's tiling microarray experiments. These resources include a comprehensive package of twenty-five command line java applications for mapping, normalizing, testing, filtering, printing, plotting, comparing, and annotating results from tiling microarry experiments.

TiMAT Resources:

Download the TiMAT package v1.6 (28 Sept 05) - TiMAT_1.6.zip
The java source code is freely available and distributed under a BSD open source license.

Read about TiMAT nomenclature, application descriptions, command line menus, output column headings, and our suggested usage.

See examples of Zeste binding regions derived from a ChIP Chip experiment.


Drosophila melanogaster Resources:

Affymetrix's unmodified bpmap file, dmel release 3.1, pre 7G antiSense.bpmap.bz2
A BLAST filtered bpmap file, dmel release 4.0, pre 7G antiSenseBlastFilteredRel4.0.bpmap.bz2
A BLAST scored bpmap file, dmel release 4.0, pre 7G antiSenseBlastScoredRel4.0.bpmap.bz2
A MUMMER filtered/ remapped bpmap file, dmel release 4.0, for 7G antiSenseMumFiltered7GRel4.0.bpmap.bz2
Combine GFF3 gene annotation, dmel release 4.0 dmel4.0Annotation.gff3.bz2
A gold standard list of CG genes with verified cDNAs goldStandardCGGeneList.txt.bz2
Fasta chromosome files, dmel release 4.0 Dmel4.0ChromFiles.tar.bz2
Precomputed Windowed BPMapFiles (needed by many TiMAT applications) 7G-675bp Pre7G-675bp
Affymetrix's binary bpmap to text bpmap-like conversion tool (Windows) ProbeExporterV2.zip
Affymetrix's binary cel to text cel conversion tool (Windows) CelFileConversion.zip

Source Code and Java Docs:

TiMAT Java Source Code SourceCode.zip
TiMAT Java Docs JavaDocs.tar.bz2

(To force a download, try right-clicking or holding down the option key while clicking a link.)


Questions, comments, suggestions: contact SuperFly



TiMAT 2005, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "TiMAT (LBNL Ref CR-2109)"

NOTICE. This software was developed under funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.