Biopython Sequence Objects

Beatriz Manso

The Biopython programming language is an open-source application programming interface (API) used both in bioinformatics software development and in everyday scripts to perform common bioinformatics tasks.

Install Biopython in the Anaconda Powershell using the following command:

conda install -c conda-forge biopython

1.Set working directory using 'os' module:

import os
os.chdir("C:/Users/manso/OneDrive - University of West London/MSc Bioinformatics - UWL/3.DSB - Data Science for Bioinformatics/Practice/DSB W4")

2.Import "Seq" from the Bio.Seq module

from Bio.Seq import Seq #seq objects
from Bio import SeqIO #SeqRecord objects

3.Make a new seq object by using a new sequence

new_seq = Seq ("AGGTACCAGGTAG")
print(new_seq)

AGGTACCAGGTAG

4.Upload Fasta file and store as a seq object

for seq_record in SeqIO.parse("TestFasta1.fa", "fasta"):
    print ("fasta header:", seq_record.id)
    print(repr(seq_record.seq))
    print("seq length", len( seq_record))

fasta header: TestFasta
Seq('AGAAAGAACAAGCTCCTCCCCATGGTAACTCGG')
seq length 33

5.Extract seq object from seq record and store it in a variable

MySeq = seq_record.seq
print(MySeq)

AGAAAGAACAAGCTCCTCCCCATGGTAACTCGG

6.Seq objects can be searched to find the first instance of a substring using the method find()

MySeq.find("AAC")

6

MySeq.find("TAG")

-1

7. Seq objects can be searched to count the non-overlapping instances of a substring using the method count()

MySeq.count("G")

7

MySeq.count("ACC")

0

8.The complement and reverse complement can be obtained of a nucelotide sequence

print(MySeq)

AGAAAGAACAAGCTCCTCCCCATGGTAACTCGG

MySeq.complement()

Seq('TCTTTCTTGTTCGAGGAGGGGTACCATTGAGCC')

MySeq.reverse_complement()

Seq('CCGAGTTACCATGGGGAGGAGCTTGTTCTTTCT')

9. Transcribe DNA sequence into RNA

MyRNA = MySeq.transcribe()

10. Transcribe RNA sequence into DNA

MyRNA.back_transcribe()

Seq('AGAAAGAACAAGCTCCTCCCCATGGTAACTCGG')

11. RNA and DNA can be translated into protein

MyRNA.translate()

Seq('RKNKLLPMVTR')

MySeq.translate()

Seq('RKNKLLPMVTR')