MAT program

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Source code (build 2.11272006) or MAT numpy version (build 3.07312009, gcc4.3 compatible) 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.

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


RepLib for new MAT ( python2.5+numpy ): BPMap for MAT (for human and mouse, you'd better use the new version RepLib above!):
  • S. pombe (Sanger 08/23/2007):                             BPMAP