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Mouse vs Xenopus Translated Blat alignments

Mouse (Mus musculus, GRCm38) and Xenopus (Xenopus tropicalis, JGI_4.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 68. Mouse was used as the reference species. After running Translated Blat, the raw Translated Blat 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
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

Mouse Xenopus
Chunk size 1,000,000 25,000
Overlap 10,000 10,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 232,673

Genome coverage (bp) Coding exon coverage (bp)
Mus musculus

Uncovered: 2,703,980,936 out of 2,730,871,774
Covered: 26,890,838 out of 2,730,871,774

Uncovered: 17,690,031 out of 35,991,038
Matches: 13,437,167 out of 35,991,038
Mismatches: 4,855,360 out of 35,991,038
Insertions: 8,480 out of 35,991,038

Xenopus tropicalis

Uncovered: 1,491,229,058 out of 1,511,717,716
Covered: 20,488,658 out of 1,511,717,716

Uncovered: 15,196,094 out of 30,481,746
Matches: 11,294,326 out of 30,481,746
Mismatches: 3,986,378 out of 30,481,746
Insertions: 4,948 out of 30,481,746