EnsemblEnsembl Home

Human vs Sloth BlastZ alignments

Human (Homo sapiens, GRCh37) and Sloth (Choloepus hoffmanni, choHof1) 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 Sloth
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: 1,600,909

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

Uncovered: 2,051,283,245 out of 3,098,825,702
Covered: 1,047,542,457 out of 3,098,825,702

Uncovered: 9,965,134 out of 35,313,516
Matches: 21,221,421 out of 35,313,516
Mismatches: 3,858,005 out of 35,313,516
Insertions: 268,956 out of 35,313,516

Choloepus hoffmanni

Uncovered: 1,502,984,329 out of 2,467,493,193
Covered: 964,508,864 out of 2,467,493,193

Uncovered: 3,997,980 out of 19,729,254
Matches: 13,950,460 out of 19,729,254
Mismatches: 1,745,623 out of 19,729,254
Insertions: 35,191 out of 19,729,254