The BDTNP has put together a variety of resources to assist in the processing and interpretation of chip-chip tiling microarray experiments, particularly those performed withAffymetrix and Nimblegen chips. These resources include a comprehensive package of Java applications for mapping, normalizing, testing, filtering, printing, plotting, comparing, and annotating results from tiling microarry experiments.

TiMAT Resources:

User Manual

User Manual focusing on main TiMAT processing pipeline; written with version 3.4


Downloads

Please note: due to file format changes with TiMAT's *cela and *celp files, versions 3.2 and later are not backwards compatible with earlier versions.

TiMAT package v3.4.4 (15 January 08) - TiMAT_3.4.4.zip
TiMAT package v3.4.3 (13 September 07) - TiMAT_3.4.3.zip
TiMAT package v3.3.1 (9 February 07) - TiMAT_3.3.1.zip
TiMAT package v3.2.1 (22 November 06) - TiMAT_3.2.1.zip
TiMAT package v3.1.2 (12 October 06) - TiMAT_3.1.2.zip
TiMAT package v3.0.1 (14 July 06) - TiMAT_3.0.1.zip
TiMAT package v2.8.5 Alpha (9 June 06) - TiMAT_2.8.5.zip


The java source code is freely available and distributed under a BSD open source license.
The source code is in with the combined with the class files, Java Docs


Additional Info



Drosophila melanogaster Resources:

tpmap file, dmel release 4.0, for 7G7GUnique.tpmap.bz2
tpmap file, dmel release 4.0, for pre 7Gpre7GUnique.tpmap.bz2
1lQ file, needed for remapping and chip QCdmelTilingArray.1lq.bz2
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
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 4.3 dmel-all-chromosome-r4.3.fasta.bz2
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

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


Questions, comments, suggestions: contact ahechmer at lbl dot gov



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.