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Human vs Mouse Lemur BlastZ alignments

Human (Homo sapiens, GRCh37) and Mouse Lemur (Microcebus murinus, micMur1) 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 Mouse Lemur
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: 1,829,640

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

Uncovered: 1,759,490,082 out of 3,098,825,702
Covered: 1,339,335,620 out of 3,098,825,702

Uncovered: 4,658,239 out of 35,313,516
Matches: 26,848,613 out of 35,313,516
Mismatches: 3,545,024 out of 35,313,516
Insertions: 261,640 out of 35,313,516

Microcebus murinus

Uncovered: 1,666,243,801 out of 2,910,103,014
Covered: 1,243,859,213 out of 2,910,103,014

Uncovered: 3,862,379 out of 26,497,276
Matches: 20,501,106 out of 26,497,276
Mismatches: 2,089,988 out of 26,497,276
Insertions: 43,803 out of 26,497,276