Questions tagged [genomes]

The entirety of an organism's hereditary information.

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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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102 views

How to explain Genome, Genes, RNA and protein in one figure to non-biologist?

I have a presentation to do where non-biologist are attending. In order to introduce a little bit my work I have to do a quick summary on genomes. So what is a genome, a gene, an mRNA and a protein. ...
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608 views

Accuracy of genome size estimation by flow cytometry

I'm working on a genome project and using an in silico k-mer analysis to estimate the size of our genome based on the available Illumina reads. The k-mer based estimate is consistent across a wide ...
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83 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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67 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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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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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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123 views

Predicting host-pathogen gene interaction networks

Background What we have are: ~20 genome sequences for a host species that come with gene annotations Several sequenced genomes for parasite/pathogens of these hosts Question What are the possible ...
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47 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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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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44 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 ...
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20 views

issues with MultiPipMaker

I would like to use MultiPipMaker for testing a genome alignment between two sequences, each sequence is in .fasta format, but the problem is that when I submit the couples of file that I need, the ...
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50 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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26 views

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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17 views

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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31 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 ...
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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 ...