Trypanosoma brucei vs Hyaloperonospora arabidopsidis Translated Blat Results

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Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) 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. Trypanosoma brucei 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: 2,797

Genome coverage (bp) Coding exon coverage (bp)
Trypanosoma brucei

Uncovered: 25,371,579 out of 25,789,186
Covered: 417,607 out of 25,789,186

Uncovered: 12,762,639 out of 13,171,744
Matches: 265,176 out of 13,171,744
Mismatches: 143,909 out of 13,171,744
Insertions: 20 out of 13,171,744

Hyaloperonospora arabidopsidis

Uncovered: 78,579,330 out of 78,897,814
Covered: 318,484 out of 78,897,814

Uncovered: 12,877,671 out of 13,171,834
Matches: 189,301 out of 13,171,834
Mismatches: 104,810 out of 13,171,834
Insertions: 52 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

Trypanosoma brucei 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}