Phytophthora infestans vs Entamoeba histolytica Translated Blat Results

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Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) 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: 2,467

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans T30-4

Uncovered: 228,210,410 out of 228,543,505
Covered: 333,095 out of 228,543,505

Uncovered: 22,148,357 out of 22,421,425
Matches: 164,319 out of 22,421,425
Mismatches: 108,710 out of 22,421,425
Insertions: 39 out of 22,421,425

Entamoeba histolytica

Uncovered: 20,625,515 out of 20,835,395
Covered: 209,880 out of 20,835,395

Uncovered: 10,039,627 out of 10,244,611
Matches: 122,828 out of 10,244,611
Mismatches: 82,143 out of 10,244,611
Insertions: 13 out of 10,244,611

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 infestans Entamoeba histolytica
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}