Human (Homo sapiens, GRCh37) and Squirrel (Spermophilus tridecemlineatus, SQUIRREL) were aligned using the BlastZ alignment algorithm (Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9) in Ensembl release 55. Human was used as the reference species. After running BlastZ , the raw BlastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.
Full list of pairwise alignments| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Masking count (M) | 50 |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default |
Number of alignment blocks: 1768345
| Genome coverage(bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
|
|
| 1,076,080,396 out of 3,098,825,702 | 28,131,393 out of 35,483,623 | |
| Squirrel |
|
|
| 986,009,629 out of 3,499,049,606 | 18,889,271 out of 23,902,824 |