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Human vs Elephant BlastZ alignments

Human (Homo sapiens, GRCh37) and Elephant (Loxodonta africana, loxAfr3) 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 57. 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Results

Number of alignment blocks: 2,339,138

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

Uncovered: 1,720,955,638 out of 3,098,825,702
Covered: 1,377,870,064 out of 3,098,825,702

Uncovered: 1,430,213 out of 35,313,516
Matches: 29,265,355 out of 35,313,516
Mismatches: 4,345,045 out of 35,313,516
Insertions: 272,903 out of 35,313,516

Loxodonta africana

Uncovered: 1,886,032,371 out of 3,196,743,967
Covered: 1,310,711,596 out of 3,196,743,967

Uncovered: 2,570,826 out of 31,407,754
Matches: 25,346,617 out of 31,407,754
Mismatches: 3,345,856 out of 31,407,754
Insertions: 144,455 out of 31,407,754