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Human vs Kangaroo rat BlastZ alignments

Human (Homo sapiens, GRCh37) and Kangaroo rat (Dipodomys ordii, dipOrd1) 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 Kangaroo rat
Chunk size 30,000,000 1,100,000
Overlap 0 100,000
Group set size 0 4,000,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 1,482,234

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

Uncovered: 2,265,219,514 out of 3,098,825,702
Covered: 833,606,188 out of 3,098,825,702

Uncovered: 5,327,935 out of 35,313,516
Matches: 24,884,821 out of 35,313,516
Mismatches: 4,706,552 out of 35,313,516
Insertions: 394,208 out of 35,313,516

Dipodomys ordii

Uncovered: 1,410,369,641 out of 2,165,294,802
Covered: 754,925,161 out of 2,165,294,802

Uncovered: 3,517,346 out of 26,615,164
Matches: 19,921,056 out of 26,615,164
Mismatches: 3,116,094 out of 26,615,164
Insertions: 60,668 out of 26,615,164