Learn Biopython: Preliminary Step Toward Bioinformatics
4.3 (7 ratings)
Course Ratings are calculated from individual students’ ratings and a variety of other signals, like age of rating and reliability, to ensure that they reflect course quality fairly and accurately.
2,876 students enrolled

Learn Biopython: Preliminary Step Toward Bioinformatics

Performing the Daily Tasks of Bioinformatics
Hot & New
4.3 (7 ratings)
Course Ratings are calculated from individual students’ ratings and a variety of other signals, like age of rating and reliability, to ensure that they reflect course quality fairly and accurately.
2,876 students enrolled
Created by Ahmed Karam
Last updated 6/2020
English
English
Current price: $23.99 Original price: $34.99 Discount: 31% off
5 hours left at this price!
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This course includes
  • 2.5 hours on-demand video
  • Full lifetime access
  • Access on mobile and TV
  • Assignments
  • Certificate of Completion
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What you'll learn
  • Understanding the Basics of Python
  • Using Biopython as a Search Engine
  • Understanding Sequence Input/Output Files
  • Performing Pairwise Sequence Alignment
  • Performing Multiple Sequence Alignment & Phylogeny
  • Performing BLAST & Working with BLAST Output
Course content
Expand all 32 lectures 02:28:19
+ Introduction & Installation
2 lectures 08:14

In this video, I would like to illustrate the value of biopython through real models and the finest types of scientific research.

Preview 03:29
Installation of Python, Pycharm, & Biopython
04:45
+ Python Basics
7 lectures 27:48
Variable Types & Basic Operators
06:30
Each of the following questions contains code, copy the code and paste it into the Python file and execute it, try explaining the results,
Variable Types
20 questions
Each of the following questions contains code, copy the code and paste it into the Python file and execute it, try explaining the results,
Variable Types
8 questions
Decision Making
04:51
We will try to use an if statement in more than one way to solve problems that codes can encounter when they are executed.
Decision Making
5 questions
Loops - While Loop
02:46
Loops - For Loop - Part 1
02:34
Loops - For Loop - Part 2
02:20
Loops - For Loop - Part 3
01:57
In this assignment, we will present some examples that would provide the principles for the use of loops.
Loops
4 questions
+ Advanced Search at NCBI
6 lectures 29:58
NCBI Databases Information
05:09
Spelling Correction
02:23
We will present more than one example to try to illustrate the value of error correction.
Spelling Correction
2 questions
Search NCBI Databases
02:26
Retrieving Document Summaries
03:23
Through questions, we will search in more than one way in the databases and emphasize the importance of using some important words to obtain summaries, through this quick and detailed presentation of these summaries you can get the required data quickly.
Search NCBI Databases & Retrieving Document Summaries
2 questions
Global Search at NCBI
01:57
Fetching Data from NCBI
14:40
+ Sequence Input/Output
5 lectures 26:45
Writing & Converting Sequence Files
06:46
Parsing GenBank Files
05:42
Writing FASTA Files
03:24
Writing GenBank Files
06:22
+ Sequence Manipulation Methods
2 lectures 08:08
Sequence Manipulation Methods - Part 1
03:59
Sequence Manipulation Methods - Part 2
04:09
+ In-Silico Central Dogma
1 lecture 03:56
Working with DNA, RNA, and Protein Sequences
03:56
+ Basic Sequence Analysis
1 lecture 03:36
Analyzing DNA, RNA, and Protein Sequences
03:36
+ Multiple Sequence Alignment & Phylogenetic Tree
3 lectures 13:00
Analyzing Sequence Data
08:22
Parsing MSA Files
02:32
Parsing Newick Files
02:06
+ NCBI BLAST
4 lectures 18:54
Online BLAST
02:20
Parsing BLAST Output - Part 1
02:27
Parsing BLAST Output - Part 2
06:07
Local BLAST
08:00
Requirements
  • There are no requirements except to insist on learning
Description

This course gives you an introduction to Python, where we covered the basics of the language, including:

  1. Basic syntax,

  2. Variable types,

  3. Basic operators,

  4. Decision making, and

  5. Loops.

Then to the stage where Python is used to explore biopython codes, and then combine them to perform routine bioinformatics tasks, and that includes:

  1. Searching and obtaining data from NCBI databases through the internet connection,

  2. Dealing with sequence files like reading, writing, and converting,

  3. Dealing with sequences like manipulation and analysis,

  4. Performing pairwise sequence alignment (global and local),

  5. Performing multiple sequence alignment (MSA), and Dealing with MSA and Newick format file, and

  6. Finally, performing BLAST online and offline then parsing the results.

Who this course is for:
  • Students and researchers dealing with DNA, RNA, or protein sequences