## Description

These tracks display the level of sequence uniqueness of the reference mm9 genome. They were generated using different window sizes and high signal will be found in areas where the sequence is unique.

## Methods

The CRG Alignability tracks shows how uniquely k-mer sequences align to a region of the genome. To generate the data, sliding windows of k-mers (where k is 36, 40, 50, 75 or 100 nts) of the human genome sequence were mapped back to the genome using the GEM mapper aligner allowing 0, 1 or 2 mismatches. For each window, a mapability score was computed (S = 1/(number of bases of match found)). The CRG Alignability tracks show how uniquely k-mer sequences align to a region of the genome. To generate the data, the GEM-mapability program has been employed. The method is equivalent to mapping sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts to produce these tracks) back to the genome using the GEM mapper aligner (up to 2 mismatches were allowed in this case). For each window, a mapability score was computed (S = 1/(number of matches found in the genome): S=1 means one match in the genome, S=0.5 is two matches in the genome, and so on). The CRG Alignability tracks were generated independently of the ENCODE project, in the framework of the GEM (GEnome Multitool) project.

## Credits

The CRG Alignability track was created by Thomas Derrien and Paolo Ribeca in Roderic Guigo's lab at the Centre for Genomic Regulation (CRG), Barcelona, Spain. TD was supported by funds from NHGRI for the ENCODE project, while PR was funded by a Consolider grant CDS2007-00050 from the Spanish Ministerio de Educación y Ciencia."