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Human vs Hedgehog BlastZ alignments

Human (Homo sapiens, GRCh37) and Hedgehog (Erinaceus europaeus, HEDGEHOG) 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 Hedgehog
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: 1,278,795

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

Uncovered: 2,486,786,439 out of 3,098,825,702
Covered: 612,039,263 out of 3,098,825,702

Uncovered: 7,172,808 out of 35,313,516
Matches: 22,973,328 out of 35,313,516
Mismatches: 4,807,575 out of 35,313,516
Insertions: 359,805 out of 35,313,516

Erinaceus europaeus

Uncovered: 2,818,429,925 out of 3,377,524,115
Covered: 559,094,190 out of 3,377,524,115

Uncovered: 4,333,202 out of 23,708,111
Matches: 16,496,310 out of 23,708,111
Mismatches: 2,823,221 out of 23,708,111
Insertions: 55,378 out of 23,708,111