Class BioSequence

java.lang.Object
org.episteme.natural.biology.genetics.BioSequence
public class BioSequence extends Object
Biological sequence (DNA, RNA, or Protein).
Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

  • Method Details

    • length

      public int length()
      Returns the length of the sequence.

    • getSequence

      public String getSequence()
      Returns the sequence string.

    • getType

      public BioSequence.Type getType()

    • complement

      public BioSequence complement()
      Returns the complement sequence (DNA only). 5'-ATGC-3' -> 5'-TACG-3' (Note: usually reverse complement is more useful)

    • reverseComplement

      public BioSequence reverseComplement()
      Returns the reverse complement sequence. 5'-ATGC-3' -> 5'-GCAT-3'

    • transcribe

      public BioSequence transcribe()
      Transcribes DNA to RNA. T -> U

    • reverseTranscribe

      public BioSequence reverseTranscribe()
      Reverse transcribes RNA to DNA. U -> T

    • translate

      public BioSequence translate()
      Translates RNA/DNA to Protein. Starts from reading frame 0.

    • gcContent

      public double gcContent()
      Calculates GC content.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object