Questions tagged [genomes]

The entirety of an organism's hereditary information.

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1answer
87 views

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 ...
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85 views

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 ...
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1answer
42 views

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 ...
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1answer
34 views

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?
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How does the availability of a reference genome aid in microsatellite analysis?

I'm planning to use microsatellites to examine fine-scale population structure between several breeding colonies of birds. Most of my DNA will be extracted from feathers and the yield isn't sufficient ...
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2answers
49 views

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: <...
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1answer
34 views

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 ...
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1answer
53 views

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 ...
2
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1answer
59 views

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 ...
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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 ...
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2answers
29 views

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 ...
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2answers
62 views

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 ...
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1answer
37 views

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 ...
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203 views

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 ...
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104 views

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 ...
2
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1answer
100 views

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 ...
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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 ...
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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 ...
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1answer
59 views

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?...
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1answer
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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 ...
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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, ...
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72 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,...
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1answer
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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?
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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 ...
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1answer
227 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 ...
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153 views

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 ...
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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 ...
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2answers
63 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 ...
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40 views

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 ...
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Any examples of a group of micro-organism that continuously spans two or more species classifications?

Are there any examples of a group of micro-organisms where two different, established species are designated and these two groups meet all aspects of the definition of species (perhaps can not ...
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1answer
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Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables ...
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1answer
214 views

Giga base or Giga byte [closed]

"we reported ~2.66- Gb genome sequence of" "we generated 191.5 Gb high quality reads" I am very confused with these two quoted lines and I am not sure about giga byte or giga base ...
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2answers
704 views

Do chromosomes change with time?

An offspring is 23 chromosomes of mother and 23 of father, if one of the mate learns say music after the birth of their first child— will their second offspring have better music skills than former? ...
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How much DNA does a species lose after post-polyploidization genome downsizing?

After whole genome duplication, diploidization takes place, right? A lot of changings in gene organization and expression involving genetic and epigenetic mechanisms (translocations, transpositions, ...
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Gene density percentage

What do we mean when we say that: Haemophilus influenza genome is 85% genic. How do we measure gene density in percentage, especially for the above-mentioned case?
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45 views

How do you sequence a tree genome? [closed]

I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a ...
3
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1answer
110 views

Interbreedability between current humans and his ancestors

I want to know the first point of time in the past when genomes have diverged so far from modern human genomes so that they both (human and ancestors) are not interbreeadable anymore and can be seen ...
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1answer
86 views

Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?

Inbreeding depression may be reduced by selection against deleterious alleles, which eliminates, or purges, them from the population. I have two questions: Is genetic purging based on random ...
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What can a human do in a short time (10-20 years) to improve their genome?

I'm wondering what can I do to make my children receive better genes? For example, can fitness, cold showering, studying etc. change my hereditary material and affect my children?
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All somatic cells contain the same genome, then how does it knows that it should develop into a specific organ?

All somatic cells contain the same genome, then how it knows that it should develop into a specific organ. In https://www.youtube.com/watch?v=aeAL6xThfL8, Joe Hanson says that each cell has the same ...
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3answers
203 views

Single copy housekeeping genes

I am working on a tool for SNP calling in polyploid plants. To test my method, I need a list of housekeeping genes common in almost all plants. For my case, these genes must be single copy (ie each HK ...
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317 views

What is Genome Folding?

Why does genome folding have such great interest? For protein folding I could say that's important because protein's functionality closely depends on its folded state, since it affects its ...
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2answers
49 views

Personal Genomic Data Samples

a quick question. I am looking for complete personal genomic data of human individuals. The only requirement for the genomic data is that it contains the complete set of SNPs of a human individual. So ...
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1answer
542 views

Are there parts of DNA that do not have genes?

A question in my genetics class is "Are the number of genes proportional to the genome size?" The answer is "no," and is it because the genome is the entirety of all the DNA in an organism, but that ...
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1answer
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Do all chromosomes in one human body contains same genome? [duplicate]

As I understand it, each nucleus of a cell contains multiple chromosomes. Each chromosome has multiple DNAs. Each DNA contains some specific gene sequences. That sequence is called Genome. My ...
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1answer
714 views

How to build a phylogenetic tree without an outgroup? [duplicate]

I have whole genome aligned sequences of four beetle populations of same species. I wish to construct a phylogenetic tree with the four. However, I am unable to find a suitable outgroup of the species,...
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3answers
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Does the genome make sense without knowledge of the ovum?

Much of the literature for laypeople seems to consider (and to spread the idea) that an animal (or a plant, I guess) is characterised by its genome. I do not know whether the same goes for more ...
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2answers
123 views

Why do two different E. coli reference genomes have different lengths?

I've downloaded two different reference genome of E. coli (E. coli K-12 MG1655: U00096.1 and E. coli K-12 MG1655: U00096.2) and they have different lengths. I searched for the meaning of reference ...
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254 views

Can a gene-expression or epigenetic 'user-history' be found in the body?

(EDITED - a lot of what I am saying is implicit and simplified. I'm not looking to recreate the numerous textbooks and scientific papers on how DNA works). As far as I can understand it, an ...
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1answer
87 views

Finding Regulatory Elements: How Have People Been Doing This?

First up, I am NOT asking about how to search for and match regulatory elements using a database. I'm asking about how people found what to search for and match in a genome, how they built those ...