What is a repetitive region?
3
0
Entering edit mode
8.1 years ago
zhangz.cs ▴ 280

After searching on the internet, I failed to find the formal definition of a repetitive region. Highly repetitive regions confuse me greatly. Could anyone give an example to explain it. What is the difference between repetitive region and element? What does segmental duplication mean? Thank for your reply in advance!

Regards,
Zhen

Assembly sequence • 2.8k views
ADD COMMENT
3
Entering edit mode
8.1 years ago

A little background reading seems to be in order, eh? Maybe start here: https://en.wikipedia.org/wiki/Segmental_duplication

The high-level summary is that all of these refer to regions of the genome that have exactly or nearly the same sequence. Large swaths of our genome are made up of duplicated sequence - things like Alus, SINE, and LINEs, just to name a few.

These make many tasks, like mapping short reads, and assembly difficult, because it's hard to determine which of the many possible regions your particular read came from.

ADD COMMENT
1
Entering edit mode
8.1 years ago
Katie D'Aco ★ 1.0k

RepeatMasker has answers to some of your questions in its FAQ section: http://www.repeatmasker.org/faq.html

Segmental Duplications - Large blocks of 10-300 kilobases which are that have been copied to another region of the genome.

ADD COMMENT
0
Entering edit mode
8.1 years ago

These terms can be difficult to search for with Google. For the strictest definitions I recommend looking up terms in the Sequence Ontology:

For example Tandem Duplication

ADD COMMENT

Login before adding your answer.

Traffic: 1096 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6