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Questions tagged [genomes]

The entirety of an organism's hereditary information.

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What is the word for a small (under 50 bp) structural variant?

What is the word for a small (under 50 bp) SV? Perhaps it is MNV (multi-nucleotide variant)? Something like microindel? I do not like SNV as "single nucleotide" is not really correct and I ...
BigMistake's user avatar
1 vote
2 answers
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Who discovered that phage phiX174 has a single-stranded genome?

I have recently read that Erwin Chargaff has discovered that the genome of phage phiX174 (ϕχ174) is single-stranded. However I could not find the paper reporting this discovery. Is there a link to the ...
Gigiux's user avatar
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What portion of the human genome is dedicated to the developement of the fetus?

I was thinking about how we don't know the function of a large portion of DNA and I thought maybe it's because it's only used during the development of the fetus
Shannon T's user avatar
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Calculation for underlying genetic value of a phenotype given parents genetic values

What is the most accurate way to calculate a child's genetic predisposition to a phenotype, given both parents' genotypic predispositions? Assume trait X is 50% heritable and controlled by an ...
BigMistake's user avatar
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semantical meaning of positions of letters in genomic sequences

here is a sequence from the human_nontata_promoters.zip dataset that represents a genome. My question is whether the position in this genome data is consequent. For example, the positional letters at ...
malocho's user avatar
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Availability of information on genes in Gnomad VCF data

Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the ...
agnesa rivkin's user avatar
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gene dosage vs copy number

In the online articles I'm reading, I see the authors mention gene dosage and copy number. My confusion is regarding if the two terms mean exactly the same thing - number of copies a gene occur in the ...
SmallChess's user avatar
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What is "Correlation of growth" according to Darwin and was he correct about it according to modern science?

What are the views that modern biologist have on Correlation of growth? I need some clarification on statement that I'm gonna mention below as well that is it reason to that as mentioned here: "...
Schnoz's user avatar
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Do we know the genome contains all the information necessary for embryonic development?

Since high school biology I've assumed that all information necessary for creating an organism is found in its genome. As Nature's Scitable site says: Deoxyribonucleic acid, more commonly known as ...
yters's user avatar
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How frequent are transposons in action? [closed]

A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic ...
Lasha Bukhnikashvili's user avatar
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Do the quantum mechanical properties of the particles that make up DNA affect mutations in the genome?

Do quantum mechanical properties of particles, such as uncertainty, probability, tunneling, and so on, affect mutations in the genome?
Арман Гаспарян's user avatar
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Why are bacterial genomes limited in size compared to eukaryotic ones?

I was looking at this graph that shows that the eukaryotic genome has "no size limit" whilst the bacterial one does. Unfortunately the graph has no reference but essentially the idea is that ...
terraregina's user avatar
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Translating either rs number or genomic position to either a residue in the DNA or in the amino acid sequence

Studying Schizophrenia and reading some papers discussing polymorphisms in the 5HT-2A receptor gene (HTR2A). Specifically, the authors mention A-1438G, T102C, his452tyr. How does one best take ...
neurosciencecalc's user avatar
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What controls the growth of a body?

Everything in our bodies is made of cells - bones, muscles, brain, blood. How do cells know how to build a body? Granted, each cell has a blueprint of the whole body in its nuleus, the genome. Does ...
Sergey Slepov's user avatar
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Understanding Contig NG50

My goal is to do a de novo assembly of a jellyfish. At the moment I'm busy checking papers that did de novo assemblies but I also got some jellyfish papers Then I stumbled accross this: Contig NG50 ...
ilam engl's user avatar
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How is the possibility of beneficial mutations ensured in the genome?

To ensure natural selection and variability, the genome must have a structure in which the occurrence of beneficial mutations has a high enough probability. But how is this ensured? The space of ...
Arman Armenpress's user avatar
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What would an organism be like if its entire genome "worked"? [closed]

It is known that a large fraction of the genome of almost any organism "does not work", that is, it does not encode any proteins and does not participate in gene expression, in protein ...
Arman Armenpress's user avatar
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1 answer
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Has life on Earth explored the entire space of genomes?

Recently I came across a 2008 article, the authors of which argue that in fact the space of protein sequences is not as large as it might seem, and that life on Earth has most likely already explored ...
Arman Armenpress's user avatar
1 vote
1 answer
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What is targeted gene disruption?

I am a bit confused about what targeted gene disruption means. I was reading this article in which they compare the Pyrococcus Furiosus genome with a genetically tractable strain P. Furiosus variant ...
Manuela's user avatar
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What are the causes of gene amplification in archaea?

I was studying this article about Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome in order to try to extrapolate some features that could ...
Manuela's user avatar
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What is the typical arrangement of amplified genes in archaea genome?

I have to check if some genes are amplified with bioinformatics tools, but, in order to do it, I need to know what this means from a biological point of view. It seems not so difficult to understand, ...
Manuela's user avatar
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How to find a model organism's standard data about proteome size and genome size?

I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc. I found www.uiprot.org and I made ...
cavalist's user avatar
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1 answer
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What does genetically tractable strain mean?

I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this ...
Manuela's user avatar
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Why do microarrays require a priori knowledge of the genome?

Reading this paper they said this: Contemporary microarrays emerged in the wake of genome sequencing projects for one obvious reason: arrays require a priori knowledge of the query genome Why do you ...
StackedPawprints's user avatar
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Common ancestry of our cells to the first unicellular cell

If we start the chapter of life with low fidelity self replicating RNAs forming exactly identical copies of themselves, which then later evolved to form the first primordial basic cells which further ...
Ruchi's user avatar
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What is the difference between mutation per base pair and mutation per genome? [closed]

Isn't genome size considered to be the number of base pairs present in DNA? So what is the difference between the mutation per base pair and mutation per genome? Are they similar or different?
Mani's user avatar
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How to calculate the occurrence of a stretch of nucleotides in a genome?

I have seen that the formula to calculate the number of times a given sequence of nucleotides occur in a target genome is derived from that to calculate the expected frequency of restriction sites: <...
Gigiux's user avatar
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Could a mutation on neutral part of genome become deleterious?

I know that silent mutations are neutral because they dont affect function of the protein/gene, and a missense mutation would. But lets say both occur on a neutral portion, could one or the other ...
Manon Valiquette's user avatar
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Is there a negative correlation between the mRNA produced by the cell and the time of extraction? [closed]

I am doing some data analysis about gene expression time series. When I plot mRNA produced by P. Furiosus cells irradiated by gamma radiation against the time of extraction, it seems that there is a ...
Manuela's user avatar
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2 votes
1 answer
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Protein-coding introns in mitochondrial genomes

I am studying the mitochondrial genome and have read that some contain introns. However, these introns code for proteins. I cannot really understand this. Could someone tell me what intron in which ...
marilu's user avatar
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Definition of "genomic adaptation"

I have encountered the term genomic adaptation in some literature (for example Sikkink et al. 2017). I am struggling to parse the term, and I have not been able to ...
Dunois's user avatar
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which specific field to study to know more about genes and genomes [closed]

I recently got interested in specific subjects : 1.Evolution 2. DNA, genomes etc and its structure 3. Abiogenesis I am a software engineer with good fundamental understanding in math & physics ...
Jasser's user avatar
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2 answers
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How can I classify the 3 clades(S, G, V) of the coronavirus that are found on GISAID?

On GISAID they classified the corona using 4 clades(S, G, V, Other). I would like to know exactly how these genomes were classified for my research. So how do you classify a coronavirus genome as ...
yuval's user avatar
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1 answer
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How much of the genotype-phenotype map do we understand in HIV?

From what I understand, viruses have very small genomes relative to those of standard model organisms used in biological research. For example, according to Wikipedia, "the HIV genome contains nine ...
kw3rti's user avatar
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Where can I find the genome of the L-strain coronavirus and the S-strain coronavirus?

I read an interesting article about two strains of the coronavirus: https://www.newscientist.com/article/2236544-coronavirus-are-there-two-strains-and-is-one-more-deadly/ I would like to know how the ...
yuval's user avatar
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10 votes
1 answer
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What causes cells to inactivate one X-chromosome?

Normally, when a cell has two X-chromosomes (female genome), one is randomly inactivated. How does the cell detect that there are two X-chromosomes in the first place? Is there some kind of protein ...
F16Falcon's user avatar
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2 votes
1 answer
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Can I execute/model a genome? [closed]

Hi I am wondering if we can execute a genome on the sub-cellular level by running it on the computer. What I mean is using the genome as data to examine by having the cells reproduce and see what ...
Null Gene's user avatar
-1 votes
3 answers
98 views

Can convergent evolution be used to explain similarity of genome of low and high Species e g. gorilla and human?

Example: 1) molecule Rhodopsin in halobacteria for producing energy from light. 2) molecule Rhodopsin for vision in human. These are said to be of different lineages and their high similarity are due ...
user56930's user avatar
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2 answers
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What's the difference between the terms "gene map" and "genome"?

It seems some sites arbitrarily restrict "gene map" to only a single chromosome, but others don't. Supposing we don't restrict it to just a single chromosome, is it different from "genome"? Are these ...
Aero's user avatar
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1 answer
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Estimate for number of genes changed in speciation between a megafauna parent and child species [closed]

At least in terms of a back-of-the-envelope calculation, what is a believable range for the number of gene changes between parent and child species to represent speciation between species of megafauna?...
Christos Hayward's user avatar
-1 votes
1 answer
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Consider gene is countable, can anyone give a concrete example of "a gene"?

gene is a countable noun but people always say genes, so what is A gene? for instance, Each chromosome contains many genes, so, which part of the chromosome of Escherichia coli could be ...
czlsws's user avatar
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1 vote
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Why don't most life forms show uniqueness in progeny? [duplicate]

I guess everyone must have observed this. Dogs, cats, and most of all insects (including mosquitoes) appear more or less the same. Why is there so little variation in their offspring, unlike humans, ...
William R. Ebenezer's user avatar
2 votes
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259 views

What are the different types of SNPs?

When I search for this online I get answers such as substitutions, deletions, insertions etc. But I mean in the sense that I have been reading different terms infront of the word SNP such as: lead SNP,...
DN1's user avatar
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1 answer
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Identifying statistically significant gene rich and gene poor regions

I am just wondering If there any adapted way of Identifying significant gene rich and gene poor regions in each chromosome for a given genome say mm10?
Biofreek's user avatar
2 votes
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What are haplotype blocks and what is the effect of hybridization on these?

In this PDF, there is a quick definition of haplotype blocks. A haplotype block is a set of closely linked alleles/markers on a chromosome that, over evolutionary time, tend to be inherited ...
M. Beausoleil's user avatar
1 vote
1 answer
1k views

What is the most genetically complex organism?

I understand that new genomes are being sequenced ever day and these answers replace themselves often; although as of today, what has been proven to be the most genetically complex organism (Other ...
Amoebob's user avatar
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1 vote
1 answer
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What does it mean by “end effects can be ignored”

I have been reading a book ( Statistics for Biology and Health) and i encountered many of following bold text. Consider a long DNA sequence of length N, where N is assumed to be so large that end ...
Naveen Gabriel's user avatar
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1 answer
381 views

Observed to Expected CpG

Observed to Expected CpG is calculated as below : Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. I also don't ...
Naveen Gabriel's user avatar
3 votes
2 answers
75 views

Difference between NCBI's /genomes and /1000genomes

Wondering what the difference is in the data hosted here: ftp://ftp-trace.ncbi.nih.gov/1000genomes ftp://ftp.ncbi.nih.gov/genomes/ Also (sidenote), would be interested to note what the difference ...
Lance's user avatar
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1 vote
1 answer
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List of genes across species (or just for humans)

Wondering if there is a place that has a list/table/database of all the genes in the human genome, and/or all the known genes in all the species we've studied so far. Something that contains any of ...
Lance's user avatar
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