Human vs Orangutan BlastZ alignments

Human (Homo sapiens, GRCh37) and Orangutan (Pongo pygmaeus, PPYG2) 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) 5000
Threshold for gapped extension (L) 5000
Threshold for alignments between gapped alignment blocks (H) 3000
Masking count (M) 10
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 1336785

Genome coverage(bp) Coding exon coverage (bp)
Human
2,020,467,968 out of 3,098,825,702 34,723,491 out of 35,483,623
Orangutan
1,956,980,453 out of 3,446,771,396 29,280,472 out of 29,861,178