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Human vs Horse BlastZ alignments

Human (Homo sapiens, GRCh37) and Horse (Equus caballus, EquCab2) 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)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
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 Horse
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} {default_soft_masking => 1}

Results

Number of alignment blocks: 1,658,371

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

Uncovered: 1,451,873,797 out of 3,098,825,702
Covered: 1,646,951,905 out of 3,098,825,702

Uncovered: 1,866,577 out of 35,313,516
Matches: 29,408,981 out of 35,313,516
Mismatches: 3,812,693 out of 35,313,516
Insertions: 225,265 out of 35,313,516

Equus caballus

Uncovered: 909,788,972 out of 2,474,912,402
Covered: 1,565,123,430 out of 2,474,912,402

Uncovered: 2,825,036 out of 31,526,203
Matches: 25,682,387 out of 31,526,203
Mismatches: 2,923,617 out of 31,526,203
Insertions: 95,163 out of 31,526,203