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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.

Configuration parameters

ParameterValue
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:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

Human Tree Shrew
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 2,131,069

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 2,019,122,533 out of 3,098,825,702
Covered: 1,079,703,169 out of 3,098,825,702

Uncovered: 6,677,597 out of 35,313,516
Matches: 24,268,557 out of 35,313,516
Mismatches: 4,061,700 out of 35,313,516
Insertions: 305,662 out of 35,313,516

Tupaia belangeri

Uncovered: 2,671,035,145 out of 3,670,324,638
Covered: 999,289,493 out of 3,670,324,638

Uncovered: 4,712,427 out of 24,447,710
Matches: 17,464,728 out of 24,447,710
Mismatches: 2,229,336 out of 24,447,710
Insertions: 41,219 out of 24,447,710