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Xenopus vs Coelacanth Translated Blat alignments

Xenopus (Xenopus tropicalis, JGI_4.2) and Coelacanth (Latimeria chalumnae, LatCha1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 66. Xenopus 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

Xenopus Coelacanth
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: 218,662

Genome coverage (bp) Coding exon coverage (bp)
Xenopus tropicalis

Uncovered: 1,484,802,820 out of 1,511,717,716
Covered: 26,914,896 out of 1,511,717,716

Uncovered: 12,997,850 out of 30,481,746
Matches: 12,889,983 out of 30,481,746
Mismatches: 4,588,402 out of 30,481,746
Insertions: 5,511 out of 30,481,746

Latimeria chalumnae

Uncovered: 2,838,799,436 out of 2,860,591,921
Covered: 21,792,485 out of 2,860,591,921

Uncovered: 15,252,685 out of 30,870,617
Matches: 11,556,653 out of 30,870,617
Mismatches: 4,054,162 out of 30,870,617
Insertions: 7,117 out of 30,870,617