Archive Ensembl HomeArchive Ensembl Home

Human vs Tree Shrew BlastZ alignments

Human (Homo sapiens, GRCh37) and Tree Shrew (Tupaia belangeri, TREESHREW) 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

Configuration parameters

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

Results

Number of alignment blocks: 2131069

Genome coverage(bp) Coding exon coverage (bp)
Human
1,079,703,169 out of 3,098,825,702 28,796,405 out of 35,483,623
Tree Shrew
999,289,493 out of 3,670,324,638 19,735,315 out of 24,447,710