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关于内容
Once we have sequenced genomes in the previous course, we would like to compare them to determine how species have evolved and what makes them different. In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. We will encounter a powerful algorithmic tool called dynamic programming that will help us determine the number of mutations that have separated the two genes/proteins. In the second half of the course, we will "zoom out" to compare entire genomes, where we see large scale mutations called genome rearrangements, seismic events that have heaved around large blocks of DNA over millions of years of evolution. Looking at the human and mouse genomes, we will ask ourselves: just as earthquakes are much more likely to occur along fault lines, are there locations in our genome that are "fragile" and more susceptible to be broken as part of genome rearrangements? We will see how combinatorial algorithms will help us answer this question. Finally, you will learn how to apply popular bioinformatics software tools to solve problems in sequence alignment, including BLAST.
课程大纲
- Week 1 - Week 1: Introduction to Sequence Alignment
Welcome to class!
If you joined us in the previous course in this Specialization, then you became an expert at assembling genomes and sequencing antibiotics. The next natural question to ask is how to compare DNA and amino acid sequences. T...
- Week 2 - Week 2: From Finding a Longest Path to Aligning DNA Strings
Welcome to Week 2 of the class!
Last week, we saw how touring around Manhattan and making change in a Roman shop help us find a longest common subsequence of two DNA or protein strings.
This week, we will study how to find a highest scoring ...
- Week 3 - Week 3: Advanced Topics in Sequence Alignment
Welcome to Week 3 of the class!
Last week, we saw how a variety of different applications of sequence alignment can all be reduced to finding the longest path in a Manhattan-like graph.
This week, we will conclude the current chapter by cons...
- Week 4 - Week 4: Genome Rearrangements and Fragility
Welcome to Week 4 of the class!
You now know how to compare two DNA (or protein) strings. But what if we wanted to compare entire genomes? When we "zoom out" to the genome level, we find that substitutions, insertions, and deletions don't tell...
- Week 5 - Week 5: Applying Genome Rearrangement Analysis to Find Genome Fragility
Last week, we asked whether there are fragile regions in the human genome. Then, we took a lengthy detour to see how to compute a distance between species genomes, a discussion that we will continue this week.
It is probably unclear how computing th...
- Week 6 - Week 6: Bioinformatics Application Challenge
In the sixth and final week of the course, we will apply sequence alignment algorithms to infer the non-ribosomal code.
教师
Pavel Pevzner
Professor
Department of Computer Science and Engineering
Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering
Nikolay Vyahhi
Visiting Scholar
Department of Computer Science and Engineering
内容设计师
加州大学圣地亚哥分校是位于加利福尼亚州圣地亚哥的一所公立赠地研究型大学。加州大学圣地亚哥分校成立于 1960 年，位于斯克里普斯海洋学研究所附近，是加州大学十个校区中最南端的一个，提供 200 多个本科和研究生学位课程，在校本科生 33,096 人，研究生 9,872 人。
加州大学圣地亚哥分校被认为是世界上最好的大学之一。多份出版物将加州大学圣地亚哥分校的生物科学系和计算机科学系评为世界前十名。
平台
Coursera是一家数字公司，提供由位于加利福尼亚州山景城的计算机教师Andrew Ng和达芙妮科勒斯坦福大学创建的大型开放式在线课程。
Coursera与顶尖大学和组织合作，在线提供一些课程，并提供许多科目的课程，包括：物理，工程，人文，医学，生物学，社会科学，数学，商业，计算机科学，数字营销，数据科学 和其他科目。
