1. BioPython http://biopython.org/wiki/Biopython Download
& Installation
Documentation

2. BioPython Key features: Sequences Sequence Annotation I/O Operations
Accessing online databases
Multiple sequence alignments
BLAST
and many many more …

3. quickstart: Sequence objects
Simple example:
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
dna_sequence = Seq('AGGCTTCTCGTA', IUPAC.unambiguous_dna)
print dna_sequence
print dna_sequence.alphabet

4. quickstart: parsing sequences
Simple example:
from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
print(seq_record.id)
print(repr(seq_record.seq))
print(len(seq_record))
file
format

5. sequence objects alphabet sequence sequences work like strings
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
dna_sequence = Seq('AGGCTTCTCGTA', IUPAC.unambiguous_dna)
for index, letter in enumerate(dna_sequence):
print("%i %s" % (index, letter))
print dna_sequence[2:7]
print dna_sequence[0::3]
print dna_sequence[1::3]
my_seq = str(dna_sequence) + “ATTAATTG”
fasta_format_string = ">Name\n%s\n" % my_seq
print(fasta_format_string)
alphabet
sequence
sequences work like strings
slicing of sequences
striding of sequences
turning sequences into strings

6. sequence objects making complements making mRNA
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC”, IUPAC.unambiguous_dna)
print my_seq
print my_seq.complement()
print my_seq.reverse_complement()
my_seq = Seq(my_seq, IUPAC.unambiguous_rna)
messenger_rna = my_seq.transcribe()
print messenger_rna
making complements
making mRNA

7. sequence objects translation translation
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG”, IUPAC.unambiguous_rna)
print messenger_rna
print messenger_rna.translate()
coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", IUPAC.unambiguous_dna)
print coding_dna.translate()
print coding_dna.translate(table = 2)
#translation tables
translation
translation
translation using different tables

8. seqRecord object .seq sequence itself, typically a Seq object.
.id primary id, string
.name common name, string
.description human readable description, string
.letter_annotations Holds per-letter-annotations using a (restricted) dictionary of additional information, Python sequence
.annotations additional information, dictionary
.features A list of SeqFeature objects with more structured information about the features on a sequence (e.g. position of genes on a genome, or domains on a protein sequence)
.dbxrefs database cross-references, string

9. seqRecord object from scratch from Bio.Seq import Seq
simple_seq = Seq("GATC")
from Bio.SeqRecord import SeqRecord
simple_seq_r = SeqRecord(simple_seq)
simple_seq_r.id = (“0001”)
simple_seq_r.name = (“MFG1”)
simple_seq_r.description = "Made up sequence”
print simple_seq_r
reading the information
from Bio import SeqIO
record = SeqIO.read("NC_ fna", "fasta")
print record

10. Sequence I/O Parsing from file from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
print(seq_record.id)
print(repr(seq_record.seq))
print(len(seq_record))
Or using an iterator:
identifiers = [seq_record.id for seq_record in SeqIO.parse("ls_orchid.fasta", ”fasta")]
print identifiers
handle
format

11. Sequence I/O Parsing from the web from Bio import Entrez
from Bio import SeqIO
Entrez. =
handle = Entrez.efetch(db="nucleotide", rettype="fasta", retmode="text", id=" ")
seq_record = SeqIO.read(handle, "fasta")
handle.close()
print("%s with %i features" % (seq_record.id, len(seq_record.features)))

12. Sequence I/O How to find sequence information from Bio import SeqIO
orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", ”fasta"))
creates Python dictionary with each entry held as a SeqRecord object in memory