From "The Uniqueome: A mappability resource for short-tag sequencing
Ryan Koehler, Hadar Issac , Nicole Cloonan,*, and Sean M. Grimmond." Bioinformatics (2010) doi: 10.1093/bioinformatics
Paper does look interesting though!
Summary: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here we present the “uniqueome”, a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data is available for human, mouse, fly, and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data.
Availability: Files, scripts, and supplementary data is available from http://grimmond.imb.uq.edu.au/uniqueome/; the ISAS uniqueome aligner is freely available from http://www.imagenix.com/