Chapter 2 - General Info About Biopython

Create a Sequence Object

from Bio.Seq import Seq;

seq = Seq("AGTACACTGGT"); # Create a seqeunce since has seq methods attached to this obj

Import Sequence from FASTA File

File From NCBI

• Go to NCBI Website to locate nucleotide sequences.
• Info about SeqIO

Import sequence and parse into list

from Bio import SeqIO

records = list(SeqIO.parse("ls_orchid.fasta", "fasta"));

print(records[0].id) # first record
print(records[-1].id) # last record

Import Sequence from GenBank File

Import sequence and parse into list

from Bio import SeqIO

records = list(SeqIO.parse("ls_orchid.gbk", "genbank")) print(records[0].id) # first record
print(records[-1].id) # last record

Chapter 9

Entrez
PubMed

Chapter 20

Project Cookbook

Project

Bio.Phylo
Phylogenetic Trees