Questions tagged [genomes]
The entirety of an organism's hereditary information.
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Does the string "...CATCAT..." appear in the DNA of Felis catus?
In Hofstadter's Gödel, Escher, Bach: An Eternal Golden Braid (GEB), the following claim appears:
...in the species Felis catus, deep probing has revealed that it is indeed possible to read the ...
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Which organism has the smallest genome length?
Which animal/plant/anything has smallest length genome?
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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 ...
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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 ...
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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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How can I find a complete human genome file?
I'm trying to figure out how I can download a file that represents the complete human DNA sequence. I don't care too much about the format – I'm able to write C++ code to parse it. FASTA seems like a ...
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Chicken Genome what are the LGE 'chromosomes'?
The chicken genome identifies two "LGE" sequences in the chicken genome. Are these distinct chromosomes or some highly variable sequence from the genome that is put in a separate sequence? I'm ...
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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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determining genome-wide exogenous binding of pathogens to host genome?
I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...
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Why does polyploidy give an evolutionary advantage?
I would like to know what advantages polyploidy holds. I have come across a few examples during my research of polyploidy, for example human adults' hearts contain 27% diploid, 71% tetraploid and 2% ...
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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 ...
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Number of transcription factor genes in the human genome
What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. ...
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Examples of intracellular parasites of medical or economic importance?
What are examples of intracellular parasites of medical or economic importance? I have read that Xanthomonas oryzae is an intracellular parasite in rice that produces proteins able to cause changes in ...
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Chromosomes are of different size but why do all chromosomes have similar GC percentage?
When I browsed NCBI I saw a pattern: even if the chromosome sizes, number of genes, and number of proteins are different, GC% in chromosomes tend to be similar. The examples are linked below.
Yeast,
...
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Importance of knowing GC Content of an organism
I was looking at the GC content percentages of few organisms. I also know calculating the GC content percentage. But, what I want to know is, what information would we get., let us suppose if human ...
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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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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 ...
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Why do some bacteria have most genes on the leading strand of the genome?
Genes in the (+) strand are black and genes in the (-)strand are red.
The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed ...
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What does conditional analysis of a SNP in a GWA study entail?
I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
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Whole genome amino acid composition tool?
I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes.
I've looked in MeSH terms database ...
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harvesting fertilized eggs from Tetraodontidae species?
I would like to know how easy/difficult it is to harvest fertilized eggs from Tetraodontidae species such as Tetraodon nigroviridis or Takifugu rubripes compared to zebrafish? Ultimately, I would like ...
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DNA modifications other than 5-mC/5-hmC/5-fC/5-caC in vertebrate genomes?
Other than 5-Methylcytosine and the more recently discovered 5-Hydroxymethyl, 5-formil and 5-carboxylcytosine DNA modifications found in DNA sequences, what are other DNA modifications present in ...
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Why do cells vary in shape and function when they have the same genome and the same organelles?
Why do cells vary in shape and function when they have the same genome and the same organelles. For example: why do all cells have nuclei but red blood cell's don't; why can't the cells of a eye ...
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Variations in Genome Sizes
Why is there wide variation in genome size amongst groups of protists, insects, amphibians and plants, but less variation within groups of mammals and reptiles?
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What species have had their genomes sequenced/are being sequenced?
The human genome project released it's first complete genome nearly ten years ago. Since then many species have also been sequenced.
I am trying to find a list of completed (and possibly ongoing/...
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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 ...
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Drosophila reference genome
Does anyone know the details about which line they are using to sequence as the Drosophila melanogaster reference genome?
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Biodiversity is restricted by genome combinatorics?
Me and some friends are interested in opinions for the following:
Conjecture
The maximum number of species must be limited by the maximum
combinatorial/permutational space that can be occupied ...
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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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Why do we need deep sequencing?
Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological ...
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What is the genome size of Saffron (Crocus sativus)?
I searched the web but cannot find an answer for my question. Has the genome size of Crocus sativus been determined?
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sex limited genome transmission
In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters ...
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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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Degree of dosage compensation in Drosophila melanogaster
In this paper the authors state that the dosage compensation seen in Drosophila is approximately twofold, but they do not provide any source or numbers (as far as I can see) for this. What is the mean ...
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Could miniaturization be used to protect endangered large species? [closed]
In some animals (like dogs) size seems like it's controlled mostly by just a few genes (IGF1, and the genes that repress it). I'm curious:
(1) Does other miniaturization takes a similar route (for ...
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Why is the frog genome so much larger than a fish's?
As we have heard in the summaries of the human ENCODE project, 80 per cent of junk DNA appears to have an essential function. Many fish have a genome with only one tenth the size of a usual vertebrate ...
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Do there exist publicly available Genome sequences of a family?
I would like to explore the genome sequence of a publicly available genome sequences of a family (like mother, father, son, daughter...). If such human genome sequences are not publicly available at ...
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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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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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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 ...
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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 ...
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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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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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Publicly available genotype data?
I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this:
...
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Is There An Initiative To Sequence The Genomes Of Critically Endangered Species?
I realize that there are many isolated efforts to sequence the genome of a particular endangered species such as the orangutan or the snow leopard. However is there a concerted effort to sequence the ...
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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 ...
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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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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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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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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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