Phytophthora parasitica vs Hyaloperonospora arabidopsidis Translated Blat Results

Back to all analyses

Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 parasitica 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: 56,012

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora parasitica P1569

Uncovered: 42,137,365 out of 55,229,644
Covered: 13,092,279 out of 55,229,644

Uncovered: 15,889,879 out of 27,601,672
Matches: 8,825,501 out of 27,601,672
Mismatches: 2,879,383 out of 27,601,672
Insertions: 6,909 out of 27,601,672

Hyaloperonospora arabidopsidis

Uncovered: 68,375,182 out of 78,897,814
Covered: 10,522,632 out of 78,897,814

Uncovered: 4,546,383 out of 13,171,834
Matches: 6,603,459 out of 13,171,834
Mismatches: 2,011,649 out of 13,171,834
Insertions: 10,343 out of 13,171,834

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

Phytophthora parasitica 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}