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所在平台: Udemy |
课程主页: https://www.udemy.com/course/learn-biopython/
课程评论：没有评论
课程名称：Biopython 课程概述：本课程内容分为两个主要部分。第一部分介绍Python编程语言的基础知识，旨在建立算法和编程语言的一般基础。具体内容包括：安装Python、PyCharm和Biopython，掌握基本语法，包括变量和行写入方法；学习五种变量类型，包括数字、字符串、列表、元组和字典；了解各种运算符类型，如算术运算符、比较运算符、赋值运算符、逻辑运算符、成员运算符和身份运算符；理解决策策略，包括使用“if...else”、“if...elif...else”以及嵌套if语句；掌握循环的基本概念，包括while循环和for循环的写作与控制。 第二部分是Biopython的介绍，这是基于Python的一个软件包，我们将在此部分运用第一部分所学的知识。内容包括：通过Entrez处理NCBI数据库，需联网，使用einfo、espell、esearch、esummary、egquery和efetch；使用seqio处理文件，写入和转换文件，详细了解两种最流行的序列文件类型的读写；通过Python处理序列，理解一些函数，如slice、find、count、len、lower、upper、replace、split、join和strip；分子转录，包括细胞转录和DNA、RNA的正、反转录，以及DNA翻译；制造DNA的互补链和反向互补链；进行简单的序列分析，包括GC含量、分子量和六个阅读框，使用nt_search在序列中查找；进行成对比对，理解并实现局部和全局比对，处理结果并理解匹配和缺口；多序列比对，执行并读取多序列比对，提取系统发育树的数据；使用BLAST在NCBI数据库中搜索序列，建立本地数据库并实现离线BLAST，详细处理结果。 该课程对希望深入学习生物信息学和Python编程的学习者非常适合。
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:Install python, pycharm, and biopython.Knowledge of basic syntax, which includes variables and line write methods in python.Knowing the five variable types, which include number, string, list, tuple, and dictionary.Knowing the operator types, including arithmetic, comparison, assignment, logical, membership, and identity.Understanding decision-making strategies, including the use of "if.. else", "if.. elif.. else" and "nested if.".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:Dealing with the NCBI database through Entrez, requires an internet connection, and we will use einfo, espell, esearch, esummary, egquery, and efetch.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.Working with sequences through python, they understand some functions such as slice, find, count, len, lower, upper, replace, split, join and strip.Transcription of molecules as cell, transcription and reverse transcription of DNA and RNA respectively, DNA translation. manufacture of complement and reverse complement of DNA.Simple basic analysis of sequences, including GC content, molecular weight, and six reading frames. search inside sequences using nt_search.Pairwise alignment, understanding, and implementing both local and global alignment. work with results and understand matches and gaps.Multiple sequence alignment, execute and read multiple sequence alignment and extract data for the phylogenetic tree.Blast, sequence search in the NCBI database. build a local database and implement blast offline. dealing with results in detail.
