Questions tagged [genomes]

The entirety of an organism's hereditary information.

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22 views

What is the strand specificity of a atac-seq?

ATAC-seq provide the open chromatin sites such as: (coordinates) chr1 10109-10357 chr1 180730-181630 chr1 191491-191736 chr1 267816-268196 ...... I can not figure out whether the coordinates are on ...
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43 views

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 ...
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106 views

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 ...
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51 views

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 ...
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93 views

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 ...
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103 views

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 ...
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40 views

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 ...
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49 views

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 ...
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1answer
79 views

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, ...
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43 views

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 ...
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194 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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94 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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47 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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37 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
54 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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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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54 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 ...
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61 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
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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 ...
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63 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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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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206 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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119 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 ...
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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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68 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 ...
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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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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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31 views

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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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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42 views

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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299 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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173 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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105 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 ...
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2answers
65 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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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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230 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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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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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 ...
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1answer
112 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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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 ...