Human vs Medaka Translated Blat alignments
Human (Homo sapiens, GRCh37) and Medaka (Oryzias latipes, MEDAKA1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 55. Human 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
| Parameter | Value |
|---|---|
| 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
| Human | Medaka | |
|---|---|---|
| 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} |
Results
Number of alignment blocks: 189,355
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Homo sapiens |
Uncovered: 3,078,306,522 out of 3,098,825,702 |
Uncovered: 20,388,166 out of 35,313,516 |
| Oryzias latipes |
Uncovered: 854,080,794 out of 868,983,502 |
Uncovered: 18,237,464 out of 30,193,605 |
