61 votes
Accepted

I just had my genome sequenced. Can someone tell me what these different file formats are?

This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology. I'm glad we encourage such questions from curious people who want to learn more. ...
Alex Reynolds's user avatar
11 votes

If a DNA letter is one of A,T,C and G, and there are 3 billion base pairs, why don't we say that there are 6 billion letters in the genome?

If a DNA letter is one of A,T,C and G, and there are 3 billion base pairs, why don't we say that there are 6 billion letters in the genome? It is a convention, and stating the actual number of ...
adjan's user avatar
  • 2,106
11 votes
Accepted

Why does human chromosome 19 have the second highest number of protein-coding genes?

This Nature paper from 2004, by Jane Grimwood et al. goes at least a long way towards giving an answer to the question of the OP. In short: there were inordinately many duplications, especially during ...
Yuri Robbers's user avatar
9 votes
Accepted

In percentage, how much is the human genome (DNA) similar to the mouse genome?

This question cannot be answered as simply as you put it, but it's not too much to elaborate on. The order of the base pairs will be drastically different, but the same proteins and amino acids will ...
Butallati's user avatar
  • 134
9 votes
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What are the potential dangers (if any) facing the twin girls recently born in China with their CCR5 gene modified?

Important notes: I am not going into the ethical aspects of editing/removing CCR5 in human embryos, neither will I discuss potential effects of introducing that mutation into the human population....
Nicolai's user avatar
  • 4,391
7 votes
Accepted

Are SNPs and alleles the same thing?

Alleles are variations of a same locus that codes for a protein (gene). These alleles can come in different forms, one of which is SNP. For example, sickle cell anemia arises from an allele of the ...
Franco Grosso's user avatar
7 votes

Is there a measure of human genetic variation, where human genetic variation can differ more than 1%?

The question makes it clear that the poster is aware of the different ways of estimating human genetic variation, and he is also no doubt aware of the fact that Wikipedia is written by “people like ...
David's user avatar
  • 25.7k
7 votes
Accepted

What were the challenges to sequencing the last 8% of the human genome that took 20 years to overcome and how was this done? (T2T Consortium)

The ~8% of the sequence that was missing was, as you say, complicated by high repeat content. Repeats make the problem of computational genome assembly hard at the best of times. Long repeat arrays ...
Maximilian Press's user avatar
5 votes
Accepted

Is it safe to publish a person's genome?

It is as safe as to publish your fingerprints. Right now, there is little that anyone can do with your genetic information but in the future, this will change. One of the feared consequences it ...
alec_djinn's user avatar
  • 3,108
5 votes

What's the longest intron in the human genome?

Short answers: Based on gencode the longest intron for protein coding transcripts, is the intron 3-4 of the transcript ENST00000465127.1 with 1,240,120 bases. Long answer: Download the main annotation ...
finswimmer's user avatar
4 votes

How many recombination events are there per generation in humans?

"On average, between two and three crossover events occur on each pair of human chromosomes during meiotic division I" according to Molecular Biology of the Cell. 4th edition by Alberts B, Johnson A, ...
pas28's user avatar
  • 41
4 votes

How much of the Neanderthal genome is living on in humans?

Even though individual humans only have around 2-5% Neanderthal genome, it's not the same 2-5% across people. In total, at least 20%, and perhaps as much as 40% of the Neanderthal genome could be ...
iayork's user avatar
  • 14.2k
4 votes

What is the strand specificity of a reference genome?

The + and - is a bioinformatics classification. The reference sequence is by default the + ...
WYSIWYG's user avatar
  • 35.6k
4 votes
Accepted

SNPs in the Human Genome

I was wondering how many SNPs there are in a single person on average A SNP is a polymorphism in the population, it is not a thing a haplotype can carry. Each individual has a given variant for any ...
Remi.b's user avatar
  • 68.1k
4 votes

Statistician confused about exact SNP data type

SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism" only means there is a variability (between individuals) in a single ...
BagiM's user avatar
  • 583
4 votes
Accepted

Human gene number distribution on different strands of the chromosomes

For humans and other eukaryotes, the convention is that the "start" of each chromosome is the end closest to the centromere: In all human reference chromosomes, as for other eukaryotes [3], ...
acvill's user avatar
  • 8,296
3 votes

What does chrUn mean in the output from a Bowtie run on human sequences?

It is for unassigned sequences. See this reference from the UCSC Genome Browser FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download11
Tara Eicher's user avatar
3 votes

What does chrUn mean in the output from a Bowtie run on human sequences?

I presume chrUn_KI270424v1 refers to a scaffold or sequence that has not yet been assigned to a chromosome. The designation after the Un (unknown or unassigned?) may refer to a particular single ...
David's user avatar
  • 25.7k
3 votes

Why does human chromosome 19 have the second highest number of protein-coding genes?

It's interesting that not only the leader 19, but also 16 and 17 follow a similar trend. Perhaps their size could be the best weight/length proportion to ensure a safe replication? Then what would ...
Rodrigo's user avatar
  • 1,300
3 votes

What is the strand specificity of a reference genome?

Answer There is no such thing as a positive or negative strand for a genome (reference or otherwise), for the simple reason that the genomes of almost all organisms contain genes in both orientations, ...
David's user avatar
  • 25.7k
3 votes

What are the potential dangers (if any) facing the twin girls recently born in China with their CCR5 gene modified?

2019-09-29 update: the answer below is based on a scientific paper that seems to have a major flaw, see https://www.statnews.com/2019/09/27/major-error-undermines-study-suggesting-change-introduced-in-...
Franck Dernoncourt's user avatar
3 votes

What would an organism be like if its entire genome "worked"?

Your question is closely related to the concept of minimal genomes, in which researchers attempt to understand the significance of genes by removing everything that isn't strictly necessary, which ...
jakebeal's user avatar
  • 6,977
2 votes

What distinguishes "coding" from "noncoding" DNA?

DNA regions coding for proteins and RNA's comprise a rather small portion of total eucaryotic DNA.They are associated with special upstream signal sequences (promoters,enchancers,"boxes"etc) ...
Dikeos Mario S.'s user avatar
2 votes
Accepted

Does GC content determine codon bias or does codon bias determine GC content

Think about it this way, the G-C content is averaged over the entire genome, and varies between different species. Whether you are dealing with prokaryotes, with relatively compact genomes, or with ...
mdperry's user avatar
  • 3,517
2 votes
Accepted

How two genomes adopt when cell goes to recipient's body from donor's body?

My previous answer was to the original question which focused on red blood cells which do not contain DNA. Now the question has been revised to focus on tissue transplantation, where the cells do ...
David's user avatar
  • 25.7k
2 votes
Accepted

How Much DNA do Siblings whose Parents are First Cousins Share?

Before I actually answer your question, let us clear up some problems in your assumptions. The fact that you expect 50% similarity in siblings is a full of several assumptions. Imagine a case of a ...
stochastic13's user avatar
  • 4,679
2 votes
Accepted

What is the relationship between DNA molecules and the chromosomes?

To cite @canadianer, I don't really understand what you're asking but the following may help you. Genome composition First of, in the genome of most eukaryote (...
Remi.b's user avatar
  • 68.1k
2 votes

HAR1 speedy mutation

Substitution rate at neutral sequences The rate of substitutions at neutral sequences is given by the mutation rate. It si a very simple and classic result. It is because the probability of each new ...
Remi.b's user avatar
  • 68.1k
2 votes

If a DNA letter is one of A,T,C and G, and there are 3 billion base pairs, why don't we say that there are 6 billion letters in the genome?

You can refer to the Human genome as haploid or diploid. The haploid genome is around 3Gb, the diploid one is 6Gb. Usually, the bare term "Human genome" refers to the haploid one. The first picture on ...
alec_djinn's user avatar
  • 3,108
2 votes

If a DNA letter is one of A,T,C and G, and there are 3 billion base pairs, why don't we say that there are 6 billion letters in the genome?

If a DNA letter is one of A,T,C and G, and there are 3 billion base pairs, why don't we say that there are 6 billion letters in the genome? We do. Just like English has 26 letters while this post ...
CircleSquared's user avatar

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