Question: explaining N50 to grand mother
0
gravatar for Prakki Rama
5.1 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

Hi, If you were asked to explain about genome and its assembly stats like N50 to a naive person, how would you explain and make them understand ? 

assembly genome • 1.5k views
ADD COMMENTlink modified 5.1 years ago by 5heikki9.0k • written 5.1 years ago by Prakki Rama2.4k
2
gravatar for Lesley Sitter
5.1 years ago by
Lesley Sitter540
Netherlands
Lesley Sitter540 wrote:

I would draw something to explain it.

Telling her that a genome is very large and that is is very hard to find out the 1:1 exact order. Therefore you sequence contigs (or genome fragments or something like that). These fragments are ordered from large to small. You then count up the large fragments until you surpassed the 50% of your total genome size.

Based on the number of fragments you counted and the total amount of fragments you have you can find out how many fragments hold the most information (index). And based on the size of the fragment that passed the 50% mark you can find out if the most information is stored in large or small fragments?

Something like that, idn how much your grandmother knows and why you would even want to explain it to her :P

ADD COMMENTlink modified 11 months ago by RamRS30k • written 5.1 years ago by Lesley Sitter540
1

I am a grandmother learning about bioinformatics. Let's not assume only the young need to know! ;-)

ADD REPLYlink written 3.2 years ago by lnkgeo5810

Actually I wanted this to know how to explain to a high school student who does not have any knowledge not grand mother. I wanted to make it as simple as possible. Yes. Seems like you need piece of paper and pen to explain it though. Thank you for answer.

ADD REPLYlink written 5.1 years ago by Prakki Rama2.4k

Just thinking, If should explain it in simple sentence. Can I just say, "the point at which is 50% of the genome lies"

ADD REPLYlink written 5.1 years ago by Prakki Rama2.4k
1
gravatar for 5heikki
5.1 years ago by
5heikki9.0k
Finland
5heikki9.0k wrote:

When you have a set of DNA sequences of different lengths and you arrange them from the shortest to the longest, then the N50 value is the length of the shortest sequence that together with all the sequences that are longer than it make up 50% of the sum of total sequence length. As Lesley suggested, you could then draw a simple figure to support learning..

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by 5heikki9.0k
1

The N50 is ordered from longest to shortest and is then the first "long" contig that passes the 50% mark, not the other way around as you mentioned. At least, that is the method used in general papers and even Wikipedia (and we all know that everything on Wikipedia is the absolute truth XD)

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Lesley Sitter540

It doesn't matter if you arrange them from the shortest to the longest or the longest to the shortest. Either way you end up with the same exact set of contigs, no?

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.1 years ago by 5heikki9.0k
1

Good point :P but doesn't your index become larger? (there are often more small contigs than large contigs) So if you show it it seems that you have a huge amount of large contigs while in fact your were just looking at it from the wrong side up.

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Lesley Sitter540

I think it does not matter how we sort either shortest to longest or vice-versa. But, the adding up the contig size to find the middle point of genome should be done from longest to shortest.

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Prakki Rama2.4k
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