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In few cases, multiple hits with diverse locations were detected due to sequence repeats.
The segemehl software detects mismatches and indels and reports multiple hits with optimal score.
If multiple hits with equal e-values were found, these were kept only when the annotations were similar (e.g., same protein in different species).
When there were multiple hits with equally low e-values, all were extracted and converted into HUGO symbols and retained for inspection.
If a region of a BES has multiple hits with many other BESs, these sequences probably correspond to novel repetitive sequences.
This iterative optimization process quickly showed that members of only the first two scaffold classes, Class I and Class II, produced multiple hits with favorable qualities.
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Genomic regions with multiple hits within single genes were further investigated using a pairwise comparison approach based on sliding windows.
To acquire a representative sampling of taxa for each organism with multiple hits, the hit with the lowest E-value was retained in the dataset.
For each organism with multiple hits, the hit with the lowest E-value was retained in the dataset; thus, one representative of each species was present in the dataset.
'Best-hit' is defined as the hit (or multiple hits tied) with the highest E-value.
'Best-hit' is defined as the hit (or multiple hits tied) with the highest E-value (E-value cutoff = 1e-5) 3) RBH Reciprocal Best Hitt.
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