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Questions tagged [genomes]

The entirety of an organism's hereditary information.

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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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1answer
34 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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0answers
28 views

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
88 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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1answer
45 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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1answer
30 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
54 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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1answer
36 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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0answers
30 views

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 ...
3
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1answer
30 views

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 ...
1
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1answer
90 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 pair. and an ...
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0answers
95 views

What is C-value for polyploid species?

I am curious to confront genome assembly sizes with flow cytometry estimates of couple of strange polyploid genomes, but I got really confused about meaning of C-value. According verbal definition ...
3
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2answers
429 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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0answers
37 views

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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1answer
89 views

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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1answer
42 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
75 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
75 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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1answer
86 views

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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1answer
733 views

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
179 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 ...
2
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0answers
255 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
48 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
352 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 ...
0
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1answer
7k views

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
481 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,...
5
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3answers
131 views

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
108 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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2answers
202 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 ...
2
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1answer
78 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 ...
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0answers
38 views

Merge NCBI and Ensembl data

Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species. Let's say I have ...
3
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1answer
118 views

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

We often give blood to another following the blood giving compatibility chart. Heart transplant and similar transplants also brings one's cell to another's body. My curiosity is, when a cell goes to ...
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2answers
448 views

What physical traits are derived from the Neanderthal DNA in human DNA?

Some researches had found that Human DNA has a bit of Neanderthal DNA. So they suggested there would have been crossing between Homo sapiens and Neanderthals. Now the Neanderthal looked a bit ...
2
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1answer
183 views

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

I was wondering if someone knows the answer to this quenstion, because I can't find a clear answer, maybe there isn't a clear answer :). question Which of these two is right? or maybe both influence ...
3
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2answers
555 views

Why does the gc content deviate from 50% in prokaryotes

I have read quite some articles but I can't figure out the main reason for gc content deviation in prokaryotes. In eukaryotes I can understand it, because the genome isn't composed at random, like ...
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1answer
919 views

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

Some guy argued with me against evolution theory, and he claimed that human and mice share 98% just like human and chimpanzee. I've tried to search online for a simple and accurate answer, but I ...
0
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1answer
51 views

Where can I find a file listing the genetic differences in humans?

I don't know much about genetics. For an arts project I'm looking for a human genome. I read that: Only about 0.1% of the genome is different among individuals, which equates to about 3 million ...
3
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3answers
157 views

How much genomic variation one usually find within a given bacterial species?

If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to ...
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2answers
43 views

Where I can download the genome sequence of various species of Fusarium?

I'm looking for genome sequence of various species of Fusarium (a kind of fungus!) on net, but I found no suitable information. Could you please help me out for this purpose? Thanks in advance
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1answer
162 views

What is difference between several mRNA RefSeq for one gene?

I'm looking for mRNA RefSeq sequences for a given gene in the UCSC genome browser by searching gene name "HLA-F" in human (scroll to Refseq genes section). There are several RefSeq mRNA for the gene, ...
3
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1answer
136 views

Can sexual selection operate in temperature dependent sex determining organisms?

Or more broadly, are distinct forms of genetic inheritance (ie. sex chromosomes) needed for sexual selection? My thinking was that since there are no sex determining loci, there could not be linkage ...
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4answers
4k views

Is our genome decaying (see “Genetic Entropy”), and, if so, is this evidence for our genome being “young”?

In the book Genetic Entropy & the Mystery of the Genome the author says that the genome cannot be old because the genome is "decaying". Decay is a very subjective term, but in this case he means ...
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3answers
8k views

What is the strand specificity of a reference genome?

It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. So here's ...
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0answers
616 views

What happens when a genome is shorter than the other? [closed]

Say there were 2 creatures of the same species. Creature 1 has a longer genome than creature 2, it may be just a few base pairs, but what would happen when the genes were crossed to create creature 3 (...
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3answers
2k views

Is the size of the genome across species roughly the same?

Chromosome number differs across species. Is the amount of DNA comparable between organisms, just being split into smaller chunks in those species with more chromosomes, or do species have different ...
3
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3answers
1k views

How to estimate a genome's size?

The genome size of human is 3.000.000.000 bp and for Arabidopsis it is 255.000.000 bp. I know these numbers because their genomes have been published. Which methods are used by scientists to estimate ...
13
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1answer
422 views

What limits chromosomal length?

What are the upper and lower limits for chromosome length? Are these limits different in different species or kingdoms? If there is any limit, which cellular or molecular factors are reasons?
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1answer
369 views

How Scientists sequence, assemble and annotate plant genomes? [closed]

I previously read this question and this paper and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and ...
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1answer
1k views

Why is it harder to sequence plant genomes than animal genomes?

Plants seem to be less complex organisms than animals, but despite that there are less plant genomes sequenced. Is that because plant genomes are more complex, for example in terms of regulatory ...
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3answers
2k views

Why reference genome is a reference?

I have heard that a reference genome such as humans is generated by randomly choosing samples from a group of donors. But why do we call the DNA sequence generated as a reference? Why should we ...