RepLib for new MAT ( python2.5+numpy ):
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.
simple repeats and
segmental duplication information for each genome