MAT program - Version 2.0 build 04/18/2006

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Source code with Installation guide

x86.Linux executable
download, uncompress and type 'MAT' on your real x86 Linux machine (not Cygwin)

 

MAT Library Files

These library files are intended for the MAT program only. You can click each array set for the layout information (which chromosomes are included in which chip).

BPMAP: Affymetrix tiling-array probes were usually designed from the repeat-masked old genome version. Some probes are not in the new genome version and some probes have multiple copies in the genome, or even match to the repeat parts of the genome. We re-mapped all the 25mer sequences from the original Affymetrix BPMAP files to the most up-to-date full genome (including repeats) using xMAN (eXtreme MApping of oligoNucleotide). We further stored the copy number (MAT will take into account this information) of each 25mer into the new BPMAP files and removed probe redundancy to ensure the same 25-mer map to no more than once within a 1 kb window along the genome.

RepLib: RepeatMasker repeats, simple repeats and segmental duplication information for each genome (optional).
 

• Human Chr21-22, chips A, B, C NCBIv35(hg17):   BPMAP RepLib
   

• Human Encode-CHIP01 NCBIv35(hg17):               BPMAP RepLib
   

• Human Encode-Ver2 NCBIv35(hg17):                    BPMAP RepLib
   

• Human Promoter Tiling Array NCBIv35(hg17):       BPMAP RepLib  NCBIv36(hg18): BPMAP RepLib
   

• Human Tiling 2.0 7-chip Set NCBIv35(hg17):         BPMAP RepLib  NCBIv36(hg18): BPMAP RepLib
   

• Human Tiling 1.0 14-chip Set NCBIv35(hg17):       BPMAP RepLib  NCBIv35(hg17):  BPMAP RepLib
   

• Mouse Promoter Tiling Array NCBIv35(mm7):        BPMAP RepLib  NCBIv36: BPMAP RepLib
   

• Mouse Tiling 2.0  7-chip Set NCBIv35(mm7):         BPMAP RepLib  NCBIv36: BPMAP  RepLib
   

• Mouse Tiling Array 1.1 Set:
   

• Arabidopsis thaliana Tiling Array (Jan2004):         BPMAP RepLib (Thank Stefan Henz)
   

• Drosophila melanogaster Tiling version 2:            dm3: BPMAP
   

• Drosophila melanogaster Tiling version 1 (BDGPv4h):            dm2: BPMAP   dm3: BPMAP
   

• C. elegans(Wormbase WS182):                             BPMAP
   

• Saccharomyces cerevisiae (Oct2003):                  BPMAP

• S. pombe (Sanger 08/23/2007):                             BPMAP