Description

This track displays the level of conservation for each of 11 zoo species, based on blastz pairwise alignments.

Methods

Blastz pairwise alignments were performed between the NISC-generated sequence for each species and the UCSC compiled human reference sequence. All sequences were RepeatMasked, where repetitive sequences were replaced with N's. This prevented alignments from extending into repetitive regions.

The strong-hits piptool was used to identify regions of conservation greater than 50 bp in length. However, for chicken, fugu, and zebrafish, the stringency was lowered to 25 bp. Gray horizontal bars denote a mapping/sequencing gap and percent identity less than 60% is not shown since it falls below the minimum y-axis value.

Credits

Many thanks to Elliott Margulies for running the blastz alignments, putting the data in the proper format, and helpful discussions.