60 votes
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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. ...
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13 votes
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Why are the genomes of Humans 99.5% the same?

In a genome that is 3 billion base pairs, a difference of 0.5% works out to a difference of 15 million bases. When a single base change can change the amino acid sequence of a protein, that can add up ...
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13 votes
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Number of transcription factor genes in the human genome

Here I will assume we are talking about eukaryotic sequence specific transcription factors (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive ...
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  • 1,720
13 votes
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Why reference genome is a reference?

The main reason is because the genetic differences between individuals of the same species are tiny. For the vast majority of studies, they can simply be ignored. Differences between individuals are ...
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12 votes
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Turning publicly available genome data into proteins

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are: Genes (eukaryotic genes anyway) are spliced to ...
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11 votes
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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 ...
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10 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 ...
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  • 2,048
9 votes
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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 ...
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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....
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  • 4,296
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 ...
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7 votes
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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 ...
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6 votes
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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 ...
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5 votes
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What is the strand specificity of a reference genome?

First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Now let's consider to sequencing data or FASTQ files. When we align ...
5 votes

Is there a known minimal stretch of DNA that can distinguish any two people in the world?

Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, ...
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  • 1,120
5 votes
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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 ...
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  • 3,018
4 votes

How many recombination events are there per generation in humans?

Back-of-the-envelope calculation The definition of the centimorgan is that it is the length of DNA in a chromosome corresponding to a 1% chance of crossover occurring. In human chromosomes 1 cM = ...
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4 votes

Is there a known minimal stretch of DNA that can distinguish any two people in the world?

When designing PCR primers we typically use a minimum length of 20 bases, because the probability of a sequence of N bases appearing by random is $\frac{1}{4^N}$, and $\frac{1}{4^{20}}$ is about 9x$10^...
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  • 5,288
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 ...
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4 votes
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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 ...
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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 ...
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  • 562
3 votes

How would you effect bulk DNA gene therapy for a human?

Let's imagine that we understood DNA programming and our genome very well and >realized that there were some significant flaws (we die, we need sleep, etc.) And >let's imagine that we understand how ...
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3 votes

What is the strand specificity of a reference genome?

The + and - is a bioinformatics classification. The reference sequence is by default the + ...
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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, ...
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3 votes
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Markers for human genetic mapping

SNPs are much denser than RFLPs and VNTRs therefore the DNA resolution is much greater with SNPs. VNTRs were historically used for linkage mapping while SNPs allowed for association studies (e.g. GWA ...
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  • 2,863
3 votes
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Percentage of understood human DNA

The devil is in the details, and therefore we cannot just state that we have understood X% of the DNA. We know e.g. that 2% of the human DNA encode proteins. And for a good number of proteins we know ...
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  • 4,070
3 votes
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List of heritability estimates in humans?

You may consider consulting the H2DB database. The database is quite new, so the number of heritability estimates is not very high at the moment (currently 225 estimates for human, 838 estimates in ...
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  • 3,488
3 votes
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Shortest strings not present in the human genome

Sequences that don't appear in a genome are called "nullomers". That article claims that there are no 10bp sequences that don't appear in the human genome, and 80 11bp sequences that don't, citing ...
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3 votes
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How do you merge SNP data with a reference genome?

First, you need to know which genome sequence does the SNP file refer to. They must have mentioned the reference sequence that they used. As others mentioned the case of ...
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3 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, ...
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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 ...
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