Bioinformatics with Biopython - Full Course | 1 hour Python for Bioinformatics tutorial

In this video I combined all Biopython/Python for Bioinformatics tutorials to make full Biopython course with Bioinformatics examples. We will cover some of Biopython functionalities, from SeqIO module where we are going to learn how to parse FASTA/FASTQ files, to working with Seq objects and using transcribe and translate methods to transform from DNA to RNA to protein. These are just few of examples in this 1 hour long Biopython course.

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Here is the list of examples/topics I cover and feel free to skip to chapter of interest to you:
0:0:10 What is Biopython?
0:00:42 SeqIO module: reading and parsing sequence files (FASTA/FASTQ)
0:03:28 Calculating GC content of sequence which is read with Biopython SeqIO module from FASTA file
0:06:17 Biopython Seq object with example of central dogma - translation and transcription
0:09:38 Checking quality of reads - reading/parsing FASTQ file
0:14:52 NCBI databases: Accessing via Biopython Entrez
0:21:12 Pairwise sequence alignment with pairwise2 module
0:31:07 Using BLAST with Biopython to align sequences
0:34:31 COVID-19 genome analysis
0:44:48 Motif objects creation in Biopython
0:49:25 Plotting sequences information: length & GC content
0:52:10 Faster reads of big sequence files with index functionality
0:58:07 Filtering sequence files

My channel is aimed at everyone interested in Data Science and Machine Learning with Python. The mission is to simplify Python concepts, one video at a time! Stay productive!

[LanaDominkovic]

Thank you for visiting my channel! If you want to support me, the best thing to do is to subscribe and to share out the content :)
Make sure to watch my other videos as well.
Thank you :)

[BiologyIsHot]

Finally a video that doesn't spend 30% of the time showing you how to use pip/conda, as if you will be able to follow anything else if you don't know how to install packages

[farzamani]

Thank you for this tutorial!
I'm new to bioinformatics and this is such a great help as a starter

[mateuslemos]

This video is awesome. Crazy to think it was uploaded 2 years ago. I can't wait to check your most recent videos!

[오신근-yk]

Thank God! that I found this video. Lana, you are an awesome teacher. I love you ❤

[evertonreid]

Great video, well explained. I cant rate it anymore its the clearest one I have found so far
Thank you lana

[fuma]

At 20:11 I ran into an error: "StreamModeError: GenBank files must be opened in text mode."
By looking at the documentation, I added retmode="text" to the efetch parameters, that seems to have solved it.

[fuma]

At 35:35 I get an import error "ImportError: cannot import name 'GC' from 'Bio.SeqUtils'"

I used:

from Bio.SeqUtils import gc_fraction
gc_fraction(covid_dna)

instead

[조바이든-rr]

wow great video! really appreciate ur effort!

[omarismail]

Splendid tutorial! I can't wait for more.
Are you going to give a tutorial of how to use BioPython with machine learning (Chapter 16 in BioPython Cookbook)? It will be really grateful and thankful.

[sabinaanibassabinaanibas]

Hi. I am looking for a good topic for my bachelor thesis in field of Bioinformatics using Pyhton. I am studying Computer Science but this relationship between informatics and biology, genetics, etc.. is so appealing, so do you guys have some ideas or advices? Thanks in advance :)

[devenwebster]

this is an amazing tutorial. But im having an issue running some of the codes. For example, in day 2 whenever I run the code to read the NCBI databases there's always a size error and I don't know why. I was wondering if it was a mac issue.

[GauravSharma-gdpd]

Hello ma'am. I am getting this error. Can you help me out?

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\USER\AppData\Local\Programs\Python\Python311\Lib\site-packages\Bio\SeqIO\__init__.py", line 625, in parse
return iterator_generator(handle)

File "C:\Users\USER\AppData\Local\Programs\Python\Python311\Lib\site-packages\Bio\SeqIO\FastaIO.py", line 187, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "C:\Users\USER\AppData\Local\Programs\Python\Python311\Lib\site-packages\Bio\SeqIO\Interfaces.py", line 64, in __init__
self.stream = open(source, "r" + mode)

FileNotFoundError: [Errno 2] No such file or directory: 'sequence.fasta.txt'