BioPython Tutorial for Bioinformatics - How I Extract ANY Sequences from a Genbank file | Part I

#bioinformatics #datascience #python

This tutorial shows you how to read genbank files and extract sequences using the python bioinformatics package, biopython

Thank me with some coffee

Support my work

Subscribe to my channels

Reach out

Download the the reference genome using this link

Notebook can be found here

How to read Genbank files

Description of genbank files

Sections of this video
00:04 Introduction
00:47 Download example genbank file
02:31 Import biopython package
02:51 Set file path
03:19 Read genbank file using biopython
03:48 Subset all genes
05:08 Get the gene of interest
12:12 Save sequence to output file

Commands Used

from Bio import SeqIO
SeqIO.parse
SeqIO.write

Extract Sequences from a FASTA file | Python for Bioinformatics

#bioinformaticsforbeginners #bioinformática #bioinformatics #python

[rachaelobeng]

Please I keep getting an error message anytime I run the code for generating the length of the gene. The error message reads” ‘genes’ not defined” . I followed everything you did, I have tried using a different machine but still. Please what could be the problem?

[elMARABIYOCHO]

Hi, can you do a tutorial on how to extract multiple protein sequences from a fast file? I only found the one for extracting one. I have over 1000 sequences that I need to extract. I can't do it one by one.

[mdumar]

Sir,
please explain how to extract protein sequence from protein Fasta file

[mariferhdzs]

hello sir, can you explain me how this notebook can be cite ?? please

[Tamirallamiro]

though this is good but it would be helpful that you could download the data directly from the site than downloading the file your self