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Tetraodon vs Xenopus Translated Blat alignments

Tetraodon (Tetraodon nigroviridis, TETRAODON8) 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 62. Tetraodon 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

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

Results

Number of alignment blocks: 160,092

Genome coverage (bp) Coding exon coverage (bp)
Tetraodon nigroviridis

Uncovered: 339,805,391 out of 358,618,246
Covered: 18,812,855 out of 358,618,246

Uncovered: 14,374,131 out of 30,080,167
Matches: 11,265,512 out of 30,080,167
Mismatches: 4,435,291 out of 30,080,167
Insertions: 5,233 out of 30,080,167

Xenopus tropicalis

Uncovered: 1,498,310,437 out of 1,511,717,716
Covered: 13,407,279 out of 1,511,717,716

Uncovered: 19,164,280 out of 30,481,746
Matches: 8,088,872 out of 30,481,746
Mismatches: 3,225,093 out of 30,481,746
Insertions: 3,501 out of 30,481,746