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Exact(2)
The hits were filtered to keep only those with minimum alignment ratio = 0.8.
All the alignments were carried out with a minimum alignment ratio of 0.93, and the minimum size of alignment of 20.
Similar(58)
We defined a number of criteria to identify orthologous sequences including minimum alignment length (200 bp), minimum sequence identity (90%), and minimum alignment proportion (> 80% of shorter sequence).
¥ Lowest common ancestor (LCA) using 1e-5 cutoff, 60% minimum identity, and a minimum alignment lenght cutoff of 15.
The parameters for inclusion were a maximum e-value cutoff of 1e-05, a minimum identity of 60%, and a minimum alignment length of 15.
Ratios well below unity can be considered hits inside gene families or low scoring false positives, only as the minimum alignment length increases can the validity of the assignment be reasonably certain.
This search identified 708 hits (E<e−10, identity ≥ 70%, and minimum alignment length >50 bp).
Minimum alignment length coverage (-L parameter) varied between 0.1 and 0.9 with step size 0.1.
An e-value cut-off of 1×10−10 and a minimum alignment length of 50 basepairs were applied.
† = maximum e-value of 1x10-5, minimum alignment length ~100.
The minimum alignment score was set at 150.
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