Biopython

Biopython, available at $49.99, has an average rating of 3.75, with 43 lectures, 5 quizzes, based on 193 reviews, and has 4311 subscribers.

You will learn about 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 This course is ideal for individuals who are Students and researchers dealing with DNA, RNA, or protein sequences It is particularly useful for Students and researchers dealing with DNA, RNA, or protein sequences.

Enroll now: Biopython

Summary

Title: Biopython

Price: $49.99

Average Rating: 3.75

Number of Lectures: 43

Number of Quizzes: 5

Number of Published Lectures: 34

Number of Published Quizzes: 5

Number of Curriculum Items: 60

Number of Published Curriculum Objects: 51

Original Price: $27.99

Quality Status: approved

Status: Live

What You Will 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

Who Should Attend

Students and researchers dealing with DNA, RNA, or protein sequences

Target Audiences

Students and researchers dealing with DNA, RNA, or protein sequences

The course content consists of two main parts. The first part deals with an introduction to python, the goal of which is to lay down the basics of algorithms and programming languages in general. The first part contains the following:

1. Install python, pycharm, and biopython.

2. Knowledge of basic syntax, which includes variables and line write methods in python.

3. Knowing the five variable types, which include number, string, list, tuple, and dictionary.

4. Knowing the operator types, including arithmetic, comparison, assignment, logical, membership, and identity.

5. Understanding decision-making strategies, including the use of “if .. else”, “if .. elif .. else” and “nested if.”.

6. Understanding loops, writing, and controlling while loop and for loop.

The second part is an introduction to biopython, which is a package based on python, so we will apply what was understood in the first part. The second part contains the following:

1. Dealing with the NCBI database through Entrez, requires an internet connection, and we will use einfo, espell, esearch, esummary, egquery, and efetch.

2. Working with files, writing, and converting files using seqio. dealing with the two most popular types of sequence files in terms of reading and writing in detail.

3. Working with sequences through python, they understand some functions such as slice, find, count, len, lower, upper, replace, split, join and strip.

4. Transcription of molecules as cell, transcription and reverse transcription of DNA and RNA respectively, DNA translation. manufacture of complement and reverse complement of DNA.

5. Simple basic analysis of sequences, including GC content, molecular weight, and six reading frames. search inside sequences using nt_search.

6. Pairwise alignment, understanding, and implementing both local and global alignment. work with results and understand matches and gaps.

7. Multiple sequence alignment, execute and read multiple sequence alignment and extract data for the phylogenetic tree.

8. Blast, sequence search in the NCBI database. build a local database and implement blast offline. dealing with results in detail.

Course Curriculum

Chapter 1: Introduction & Installation

Lecture 1: Introduction to Python & Python Installation

Lecture 2: Python Running Modes: Interactive mode

Lecture 3: Python Running Modes: Script Mode

Lecture 4: Python Running Modes: IDE

Chapter 2: Python Basics

Lecture 1: Basic Syntax

Lecture 2: Data Types

Lecture 3: Basic Operators

Lecture 4: Accessing Python Data Items

Lecture 5: Problem-Solving

Lecture 6: Decision Making

Lecture 7: Loops

Chapter 3: Advanced Search at NCBI

Lecture 1: NCBI Databases Information

Lecture 2: Spelling Correction

Lecture 3: Search NCBI Databases

Lecture 4: Retrieving Document Summaries

Lecture 5: Global Search at NCBI

Lecture 6: Fetching Data from NCBI

Chapter 4: Sequence Input/Output

Lecture 1: Writing & Converting Sequence Files

Lecture 2: Parsing FASTA Files

Lecture 3: Parsing GenBank Files

Lecture 4: Writing FASTA Files

Lecture 5: Writing GenBank Files

Chapter 5: Sequence Manipulation Methods

Lecture 1: Sequence Manipulation Methods – Part 1

Lecture 2: Sequence Manipulation Methods – Part 2

Chapter 6: In-Silico Central Dogma

Lecture 1: Working with DNA, RNA, and Protein Sequences

Chapter 7: Basic Sequence Analysis

Lecture 1: Analyzing DNA, RNA, and Protein Sequences

Chapter 8: Pairwise Sequence Alignment

Lecture 1: Global & Local Alignment

Chapter 9: Multiple Sequence Alignment & Phylogenetic Tree

Lecture 1: Analyzing Sequence Data

Lecture 2: Parsing MSA Files

Lecture 3: Parsing Newick Files

Chapter 10: NCBI BLAST

Lecture 1: Online BLAST

Lecture 2: Parsing BLAST Output – Part 1

Lecture 3: Parsing BLAST Output – Part 2

Lecture 4: Local BLAST

Instructors

Ahmed Karam, M.Sc.
Bioinformatics and Genomics Instructor

Rating Distribution

1 stars: 7 votes

2 stars: 11 votes

3 stars: 35 votes

4 stars: 72 votes

5 stars: 68 votes

Frequently Asked Questions

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You can view and review the lecture materials indefinitely, like an on-demand channel.

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