luispedro

A very simple reader/writer for FASTA encoded DNA sequences.

# -*- coding: utf-8 -*-
# Copyright  2006 INESC/ID
# Written by Luís Pedro Coelho 
#
# Licence: MIT Licence:
#
#   Permission is hereby granted, free of charge, to any person obtaining a copy of
#   this software and associated documentation files (the "Software"), to deal in
#   the Software without restriction, including without limitation the rights to
#   use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
  

What are suffix trees?

Suffix trees are a tree representation of a string and all its suffixes. Consider the string mississippi$. It is convenient to make sure the strning ends in a symbol not found elsewhere. The suffixes of mississippi$ are:

• mississippi$
• ississippi$
• ssissippi$
• issippi$
• ssippi$
• sippi$
• ippi$
• ppi$
• pi$
• i$
• $

In tree form, this becomes: