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Human vs Hyrax BlastZ alignments

Human (Homo sapiens, GRCh37) and Hyrax (Procavia capensis, proCap1) 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 Hyrax
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: 1,810,427

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

Uncovered: 2,160,845,606 out of 3,098,825,702
Covered: 937,980,096 out of 3,098,825,702

Uncovered: 5,219,073 out of 35,313,516
Matches: 25,057,716 out of 35,313,516
Mismatches: 4,718,456 out of 35,313,516
Insertions: 318,271 out of 35,313,516

Procavia capensis

Uncovered: 2,124,257,182 out of 2,993,323,063
Covered: 869,065,881 out of 2,993,323,063

Uncovered: 3,941,949 out of 27,168,923
Matches: 20,048,844 out of 27,168,923
Mismatches: 3,116,113 out of 27,168,923
Insertions: 62,017 out of 27,168,923