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Sequences containing ambiguous symbols were discarded.
For ambiguous symbols in base or test profiles, the maximum rates of matching nucleotides are used.
By using ambiguous symbols, less triplets are formed for each amino acid when compared with the non-ambiguous symbol case.
Basically, the score of pairing two ambiguous symbols is the maximum over all substitution scores for all pairs of nucleotides from the respective sets.
For the reconstruction of the non-ambiguous putative DNA sequences at traceback, the actual pair of nucleotides that have the highest substitution score from the sets corresponding to two paired ambiguous symbols is required.
These are easily obtained for each pair of ambiguous symbols as (11) In this section we have presented a general framework that helps to compute a translation dependent scoring function for DNA sequence pairs, parametrized by a codon substitution model and an evolutionary time measured in expected number of mutations per codon.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com