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Human vs Opossum BlastZ alignments

Human (Homo sapiens, GRCh37) and Opossum (Monodelphis domestica, BROADO5) 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)2200
Threshold for gapped extension (L)10000
Threshold for alignments between gapped alignment blocks (H)2000
Masking count (M)50
Seed and Transition value (T)1
Scoring matrix (Q)$ENSEMBL_CVS_ROOT_DIR/ensembl-compara/scripts/pipeline/opossum.matrix

Chunking parameters

Human Opossum
Chunk size 10,000,000 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: 742,339

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

Uncovered: 2,768,065,495 out of 3,098,825,702
Covered: 330,760,207 out of 3,098,825,702

Uncovered: 4,877,328 out of 35,313,516
Matches: 23,365,752 out of 35,313,516
Mismatches: 6,714,241 out of 35,313,516
Insertions: 356,195 out of 35,313,516

Monodelphis domestica

Uncovered: 3,300,911,452 out of 3,605,631,728
Covered: 304,720,276 out of 3,605,631,728

Uncovered: 7,103,758 out of 33,971,162
Matches: 0 out of 33,971,162
Mismatches: 26,867,404 out of 33,971,162
Insertions: 0 out of 33,971,162