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Human vs Dolphin BlastZ alignments

Human (Homo sapiens, GRCh37) and Dolphin (Tursiops truncatus, turTru1) 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 Dolphin
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: 1,965,027

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

Uncovered: 1,653,630,447 out of 3,098,825,702
Covered: 1,445,195,255 out of 3,098,825,702

Uncovered: 2,538,993 out of 35,313,516
Matches: 28,366,907 out of 35,313,516
Mismatches: 4,097,815 out of 35,313,516
Insertions: 309,801 out of 35,313,516

Tursiops truncatus

Uncovered: 1,172,502,758 out of 2,521,907,548
Covered: 1,349,404,790 out of 2,521,907,548

Uncovered: 1,636,201 out of 28,463,360
Matches: 23,921,097 out of 28,463,360
Mismatches: 2,848,272 out of 28,463,360
Insertions: 57,790 out of 28,463,360