SS::ProteinSequence Class Reference

class representing a protein sequence with optional informations about intron postions More...

#include <pp_simscore.hh>

Public Member Functions
	ProteinSequence (const char *fileName)
char &	operator[] (int n)
int	length ()
int	intronAt (int i)
int	intronsInRange (int start, int end)

Detailed Description

class representing a protein sequence with optional informations about intron postions

The protein sequence has to be in fasta file format. The optional intron informations must be attached to the protein sequence. Format structure:

  >protein sequence header
  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
  XXXXXXX protein sequence XXXXXXXXXXX
  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

  [Introns]
  # index of the position after which an intron occures | residual nucleotides before the intron
  2 0
  5 1
  30 2
  104 1
*

The amino acids of the protein sequence can be accessed by [] with their position in the sequence. With intronAt() it can be checked if there is an intron at a position The number of introns in a specific frame can be determined with intronsInRange(start, end) For example: intronsInRange(3, 104) = 2

Author

Lars Gabriel

---

The documentation for this class was generated from the following files:

• include/pp_simscore.hh
• src/pp_simscore.cc