Phytophthora infestans vs Hyaloperonospora arabidopsidis Translated Blat Results
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Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Phytophthora infestans 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.
Results
Number of alignment blocks: 65,634
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Phytophthora infestans T30-4 |
Uncovered: 214,520,970 out of 228,543,505 |
Uncovered: 11,300,014 out of 22,421,425 |
Hyaloperonospora arabidopsidis |
Uncovered: 68,768,507 out of 78,897,814 |
Uncovered: 4,691,485 out of 13,171,834 |
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
Phytophthora infestans | Hyaloperonospora arabidopsidis | |
---|---|---|
Chunk size | 1,000,000 | 1,000,000 |
Overlap | 10,000 | 10,000 |
Group set size | 100,000,000 | 100,000,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |