- subsequence (Sequence seq, int beg, int end) — returns the subsequence between the “beg” and “end” parameters.
- complement (Sequence seq) — returns the complement sequence.
- translate (Sequence seq, int offset = 0) — returns one of the three sequence translations. Which one is returned is determined by the “offset” parameter.
- size (Sequence seq) — returns the length of the sequence.
- getName (Sequence seq) — returns the name of the sequence.
- alphabetType (Sequence seq) — returns the alphabet of the sequence.
- charAt (Sequebce seq, int ind) — returns the symbol located in the “ind” position of the sequence.
- hasQuality (Sequence seq) — determines whether the sequence has the “Quality” parameter.
- getMinimumQuality (Sequence seq) — returns the minimum value of the “Quality”.
- isAmino(Sequence seq) — returns true if it is amino acid sequence.
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