Revision as of 17:37, 19 March 2009

The Bio.Seq module in Biopython provides a few sequence related classes, the Seq object and the MutableSeq object, plus some general purpose sequence functions. In addition to this wiki page, there is a whole chapter in the Tutorial (PDF) on this topic.

In Biopython, sequences are usually held as Seq objects, which hold the sequence string and an associated alphabet.

If you need to store additional information like a sequence identifer or name, or even more details like a description or annotation, then we use a SeqRecord object instead. These are the sequence records used by the SeqIO module for reading and writing sequence files.

The Seq Object

The Seq object essentially combines a Python string with an (optional) biological alphabet. For example:

>>> from Bio.Seq import Seq
>>> my_seq = Seq("AGTACACTGGT")
>>> my_seq
Seq('AGTACACTGGT', Alphabet())
>>> my_seq.alphabet
Alphabet()

In the above example, we haven't specified an alphabet so we end up with a default generic alphabet. Biopython doesn't know if this is a nucleotide sequence or a protein rich in alanines, glycines, cysteines and threonines. If you know, you should supply this information:

>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna, generic_protein
>>> my_seq = Seq("AGTACACTGGT")
>>> my_seq
Seq('AGTACACTGGT', Alphabet())
>>> my_dna = Seq("AGTACACTGGT", generic_dna)
>>> my_dna
Seq('AGTACACTGGT', DNAAlphabet())
>>> my_protein = Seq("AGTACACTGGT", generic_protein)
>>> my_protein
Seq('AGTACACTGGT', ProteinAlphabet())

Why is this important? Well it can catch some errors for you - you wouldn't want to accidentally try and combine a DNA sequence with a protein would you:

>>> my_protein + my_dna
Traceback (most recent call last):
...
TypeError: Incompatable alphabets ProteinAlphabet() and DNAAlphabet()

Biopython will also catch things like trying to use nucleotide only methods like translation (see below) on a protein sequence.