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Length coverage of aligned transcript was examined (Fig. 1A).
The final phylogenetic assignment was expressed in percentage of total genes length coverage.
Minimum alignment length coverage (-L parameter) varied between 0.1 and 0.9 with step size 0.1.
We used equal or higher than 98% identity and 70% exon length coverage as alignment criteria to determine the match of an EST with a particular exon sequence.
CCS (57× length coverage) reads were used for correction.
An analysis of the protein length coverage for An.
A considerable improvement of protein length coverage was observed in orthologs (average protein length coverage was 74%), when compared to the protein coverage of the overall dataset (average protein length coverage of 53%).
Other clustering criteria were: 90% minimum length coverage and 10-6 cut-off e-value.
The numbers on 100% and 80% of the length coverage of top database hits were counted.
(i) E < 1.0 × 10−, (ii) sequences identify >40% and (iii) aligned sequence length coverage >40%.
Hits with Z-scores ≥ 7.5 and 60%% query length coverage were regarded as remote homologues.
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