(:source lang=python:)

""" Sequences in biopython """

""" Biopython is a collection of modules for Python bioinformatics programing. Some of its capabilities that you may find useful are: - Handling sequences and alignments - Parsing a large variety of database and data formats - Interfacing with databases - Motif analysis """

from Bio.Seq import Seq

1. Seq is biopython's class for storing biological sequences

my_seq = Seq("AGTACACTGGT")

1. note the difference between

print my_seq

1. and

my_seq

1. we didn't specify an alphabet so it's

my_seq.alphabet

1. here's some of the functionality of a sequence object:

my_seq.reverse_complement() my_seq.translate()

1. you can specify an alphabet when creating a sequence object:

from Bio.Alphabet import IUPAC my_seq = Seq("AGTACACTGGT", IUPAC.unambiguous_dna)

1. let's look at the alphabet:

my_seq.alphabet

my_dna = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC", IUPAC.unambiguous.dna) my_rna = my_dna.transcribe() my_prot = my_rna.translate() seq = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", IUPAC.unambiguous_rna) seq.translate() seq.translate(to_stop=True)

from Bio.Alphabet import IUPAC from Bio.SeqUtils import GC my_seq = Seq('GATCGATGGGCCTATATAGGATCGAAAATCGC', IUPAC.unambiguous_dna) print GC(my_seq)

from Bio.Alphabet import IUPAC cam1 = Seq("MADQLTDEQISEFKEAFSLFDKDGDGCITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLNLMAKKMKDTDSEEELKEAFRVFDKDQNGFISAAELRHVMTNLGEKLTDEEVEEMIREADVDGDGQINYEEFVKIMMAK", IUPAC.protein) cam1.alphabet

1. In many ways a sequence object behaves like a string.
2. You can iterate over its letters:

for amino_acid in cam1 :

    print amino_acid,

1. You can index it like a string:

print cam1[0] print cam1[-1]

1. and create slices:

cam_slice = cam1[10:20] print cam_slice

1. note that a slice of a sequence object is a sequence object of the same type
2. you can add sequences like you would strings:

cam1 + cam1

1. what do you think would happen if we tried to add a dna and a protein sequence?
2. A Seq object is immutable. There is also a mutable version called MutableSeq

(:sourceend:)