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Rat vs Xenopus Translated Blat alignments

Rat (Rattus norvegicus, Rnor_5.0) 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 70. Rat 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

Rat 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: 241,810

Genome coverage (bp) Coding exon coverage (bp)
Rattus norvegicus

Uncovered: 2,882,066,440 out of 2,909,698,938
Covered: 27,632,498 out of 2,909,698,938

Uncovered: 16,206,898 out of 34,224,882
Matches: 13,231,418 out of 34,224,882
Mismatches: 4,778,080 out of 34,224,882
Insertions: 8,486 out of 34,224,882

Xenopus tropicalis

Uncovered: 1,491,423,098 out of 1,511,717,716
Covered: 20,294,618 out of 1,511,717,716

Uncovered: 15,312,708 out of 30,481,746
Matches: 11,199,282 out of 30,481,746
Mismatches: 3,964,750 out of 30,481,746
Insertions: 5,006 out of 30,481,746