SEQ -BIOPYTHON.pptx

BIOPYTHON FOR BIOINFORMATICS
AN INTRODUCTION
Version 1.81
Seq
Seq Object as String
Seq Annotation
Biopython | Programming for Bioinformatics | Seq 1
Babita Neupane
M.Sc.Bioinformatics | Pokhara University
Friday, September 8, 2023 1

Biological Concept
Nucleoside
Nucleotide
Nucleic Acid
DNA & RNA
mRNA
Proteins
Sequence
Transcription
Translation
Codons
Friday, September 8, 2023 Biopython | Programming for Bioinformatics | Seq 2

Why do bioinformatician need Biopython Programming ?
Data
Management
Sequence
Analysis
Parsing and
Writing File
Formats
Phylogenetics
Analysis
Structural
Biology
Huge libraries
Rich
Communities
Research

Getting Started With Biopython
Installing Biopython
i. Open Python Editor
ii. Pip install biopython
Let’s learn Biopython ☺
PS: Biopython is case sensitive.

What are Sequence ??
Forms of Sequence
 Genomic DNA
 Coding Sequences (Exons)
 Introns
 Promoters
 Enhancers
 Silencers
 Transposable Elements
 mRNA (Messenger RNA)
 rRNA (Ribosomal RNA)
 tRNA (Transfer RNA)
 miRNA (MicroRNA)
 snRNA (Small Nuclear RNA)
 snoRNA (Small Nucleolar RNA)
 Protein Sequences (Amino Acid
Sequences)
Central object in
Bioinformatics.
Fundamental class used for
working with biological
sequences, such as DNA,
RNA, and protein sequences.

Sequence acts like Strings

It is a module provided by Biopython
that defines the Seq class.
The Seq class provides various methods
and attributes for manipulating and
analyzing these sequences.
To use this module for the first time we
have to import Bio.Seq from Biopython.
What can we do with Bio.Seq ?
 Seq()
 complement()
 reverse_complement()
 transcribe()
 translate()
 count()
 find()
 split()
 join()
What is Bio.Seq ?

Seq()
To create sequence class, we use seq() function.
If we don’t use Seq function, it act like string and seq function are restricted to string.

complement()
 Use to find complementary strand
of DNA.
 A= T or U
 C=G

reverse_complement()
This function first reverse the sequence and give complement of
the seq.
Why do we need this ?
 Primarily in Primer Designing designed to bind specific region of
DNA template; designing small interfering RNA (siRNA)
molecules to target specific messenger RNA for gene silencing
and many more and many more.

transcribe()
Given the coding sequence , it transcribes
DNA into mRNA.
Be careful with the end of seq as sequence
are read in direction 5’end to 3’end.

back_transcribe()
To convert the given RNA sequence back into the corresponding DNA
sequence .

translate()
To find amino acid sequence
from transcribed mRNA or
coding strand directly.
‘*’ identifies stop codon
"UAA," "UAG," and "UGA“.

translate() using CodonTable from Bio.Data module
Translate() function use standard codon table by default.
We can specify translate using specific codon table.
Codon table are different for different organism due to codon
usage discrepancy.

CodonTable
CodonTable have various attributes regarding
genetic codons.
Importing and using those attributes can be
obtained using specific functions.

count()
Used to count total number of
alphabets (nucleotides/amino acid
from the sequence.
Not unique feature of Biopython.
Example:

find()
Use to find index of desired seq(starts
from 0 and locate position of first alphabet
of desired seq.
Give result based on first search
Use loop to find location of the target
seq/s.

split()
To split seq given ref seq .
Ref seq can be single or multiple based on your choice.
Cleave sequences bu.

Concatenating Sequences
Used to add sequences.
Adding individual
sequences.
Adding seq from sequence
list
 Adding seq list with
specific seq (can be
repeated)

Changing cases
Similarly like in python
Using ” .lower()” & “.upper()”

Comparing Seq Objects
Equality(==, !=)
Ordering(<, <=, > , >=) #lexicographic order
Length comparison

MutableSeq Object
Seq are immutable.
To modify seq this MutableSeq allow us
to add , remove, reverse or change the
seq.

Turning Seq Objects into Strings
Easy data representation, easy &
compatible writing and
manipulating sequence files,
visualizations, simplification &
easy usage.

Working with Strings directly
Can access function of seq in
string object directly using
function as given in figure.

Parsing seq files in Biopython

Changing type
of seq files and
Accessing
changed file

2. The Bio.SeqRecord Module
This module provides the
SeqRecord class, which is a
fundamental data structure for
representing biological sequence
records.
An SeqRecord object have
attributes like seq, id,
description, annotations,
features, letter_annotations,
name, dbxrefs, annotations, and
more.
What can we do using SeqRecord class ??

Creating SeqRecord object : from scratch
We can combine a Seq object with
additional metadata and annotations with
the help of this module as shown in
example.

SeqRecord object from FASTA files
 Contain no records for dbxrefs,
annotations, letter_annotations &
features.

SeqRecord
object
from
GenBank
files

THANK YOU !!

SEQ -BIOPYTHON.pptx

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