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5

According to the HGVS guidelines, a letter prefix should be used to indicate the reference sequence used. Accepted prefixes are: “g.” for a genomic reference sequence “m.” for a mitochondrial reference sequence “c.” for a coding DNA reference sequence “n.” for a non-coding DNA reference sequence “r.” for an RNA reference sequence (transcript) “p.” for a ...


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ID mapping This is called ID mapping. It used to be a headache as programmatic access was the only real way, but it is pretty trivial these days. As mentioned in the comments, by far the most popular and easy method is to use Uniprot's list uploader for mapping. The corresponding publication can be found here. You must convert from Gene name to Uniprot KB ...


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Genetic information is the heritable information used by organisms to guide their self-assembly. It's why traits can persist across generations. DNA is, by far, the primary material used (by life) to encode genetic information, but it's not the only one. RNA is a pretty common alternative to DNA. If we're looking to Wikipedia, this is actually referred to (...


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Briefly speaking you expect more or less uniform coverage for reads. So if you see a systematic difference in quality scores or coverage for minor and major alleles or for forward and reverse strand, it could be an SNV, but most likely it is a technical issue. That's a 'dubious variant'. A lot of such biases are described in "Genotype and SNP calling from ...


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If you aren't digesting prior to amplification, sure. Nothing in PCR cares about whether or not some other protein interacts with the site. There are thousands of restriction enzymes in nature. No one would ever be able to do PCR if you had to avoid every single potential restriction site.


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Mendel's laws were very basic to aid in the comprehension of genetics. You think of Mendel's genes as an +- pair where + is dominant and - is recessive, making our +- gene produce offspring with the + trait but still being a carrier of the - trait. However, when it comes skin colour, eye colour, hair colour, height, tendency to muscle growth, and a ...


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My interpretation of the first question is why do traits determined by the environment appear to be equally similar among monozygotic and dizygotic twins in these twin studies. The studies he is talking about look at twins that are separated and adopted in to different families. These different families provide a different environment for either twin, and ...


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Until this study, medical dogma had been that when a bacterium develops resistance to a drug, it becomes weaker as a human pathogen. According to that very rosy scenario, drug-resistant strains should eventually extinguish themselves in the environment, because they can't compete with the original, drug-susceptible organism.


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This question is a bit broad. You have to understand a lot of concepts to figure out the nature of the allele. I'll just point out some basics: If an allele is dominant it should affect both males and females equally (not X-linked) If one of the parents shows the trait (while other does not) then at least one offspring should show the trait (basic ...


0

Briefly, we know of many mechanisms by which genomes can get larger. Tetrapods had at least two complete genome doublings in their history; transposons expand; retroviruses insert; partial duplications lead to pseudogenes. And these expansion mechanisms can be fast -- full genome duplications double size in a single generation. But we know of very few ...


2

"Junk DNA" is more aptly named noncoding DNA. This is defined as any DNA region that does not encode for a gene or more precisely is not within an open reading frame. In the human genome over 98% consists of noncoding DNA. However the more we learn about molecular biology the more we understand the biological function and importance of noncoding DNA. ...


1

Interpretation of the question You ask two things: 1. the number of nucleic acid bases that constitutes a gene, 2. (implied) how the size of genes are defined. The first question appears strangely naïve, but the second suggests this may be a misunderstanding. I therefore intend to start there. How are the limits of a gene defined? Genes are defined in ...


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Is there an agreed-upon definition as to how many nucleobases constitute a gene? If not, why not? There is no such definition. A gene is a region of the DNA that is transcribed. Typically a gene should have a transcription start site dictated by a promoter and a transcription stop site marked by termination signals (like terminators and poly-A signal ...


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How are gene size defined? DNA is made of 4 nucleotides A,T,C and G. A series of such nucleotide make up any section of the genome including the genes. The number of nucleotide in a gene is what we call the gene size. Of course, one might discuss on the definition of the exact beginning and end (and methods to determine them) of a gene but this is a ...


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Even though I am not sure I understand your question completely, I want to try to explain to you the genetic difference between humans and chimpanzees. I will work through your questions: We share 98.5% genes with chimps ,so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred base pairs on ...


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The genome is the complete set of DNA in an organism, including genes and non-gene sequences of base pairs (bp).1 Each codon of three base pairs in a DNA sequence specifies one of twenty different amino acids. There are four available bases in DNA; Adenine (A), Thymine (T), Guanine (G), and Cytosine (C). Four letters taken three at a time (where order ...


1

During meiosis, the independent assortment will be made first and then cross over will be made. No, independent assortment occurs after crossing over. Crossing over occurs in prophase I while independent assortment occurs in metaphase I and anaphase I. I am so confused, what is the difference between this two process? During prophase I, a process ...


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This is a very rough draft about the case, not verified, and should not be used for any medical conditions. Ask your own doctor. It is just for demonstrating some Mathematics and genetic passing generally. Condition: Muscular atrophy Differential conditions: TODO Support: history of genetic passing in -1 and -3 generations Disease Muscular atrophy as a ...


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Your first picture shows a chromosome that has been (1) condensed and (2) undergone DNA replication. During G1 interphase (normal cell activity; not dividing), your chromosomes actually do not look like either of the pictures. They look more like a mass of noodles (called chromatin; look at the image provided below); it is only during prophase (step 1 of ...


1

The first picture you posted represent a pair of chromosomes. The second one represent a single chromosome. Humans have 46 single chromosomes that can be paired in 23 pairs. In this picture, https://en.wikipedia.org/wiki/Chromosome#/media/File:NHGRI_human_male_karyotype.png, you can see the 46 human chromosomes grouped in 23 pairs. Note that the last pair is ...


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When a cell isn't dividing , the DNA is decondensed. So, you can't say what type of chromosomes are present in non-dividing human cells. But just to clarify ; it can be said if a human cell's DNA condenses into chromosome(without replication) , it will look like 46 chromosomes of image 2. If it condenses after replication, it will look like 46 chromosomes ...


-3

46 double structures during cell division. Both your images are chromosomes. Around the beginning of Prophase(cell division) the 2 sister chromatids are distinct.


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It is common in biology to use a virus to deliver new genetic information to a cell. Such a virus is called a viral vector. Retroviruses can be used to enable the viral DNA to be incorporated into the cell's genome. Usually viral genes are removed, making the virus unable to replicate once the cell is infected 1. Using viral vectors in vivo to "correct" ...


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At least PacBio do provide some example datasets on their DevNet resource. You should be able to get a lot of different Illumina data from the public data in BaseSpace. I am not sure where to look for official samples from Roche 454, but I wouldn't bother too much as it is discontinued anyway. Rather go for MinIon or IonTorrent data, if you want more.


1

Certainly it is not necessarily the case that having two of the same allele is a bad thing - if there is a "bad" allele then there is a "good" allele. It can be that the heterozygote is equal, better than, or worse than either homozygote. When the heterozygote is fitter than both homozygotes it is called heterosis and, when this is the case, outbreeding/...


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The phrasing in quite unclear and I would not be able to comment on it. In short: yes, hybridization can cause offspring to have either particularly low or particularly high fitness. Hybrid depression refers to cases where hybrids have low fitness while heterosis or hybrid vigour refers to cases where hybrids have a higher fitness than any of the two parent ...


1

It depends on the animal, some can get it, others cannot. Down syndrome is the result of an extra copy of the twenty first human chromosome. So, it is a rather humanly genetic problem. However, the closer an animal is to humans, the greater the chance of it being at risk of suffering from down syndrome. There have been several chimpanzees found ...


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Animals can be generated with genetic defects similar to Down Syndrome, but not that exact condition, except in the case of great apes. Down Syndrome is a kind of defect called a chromosomal abnormality, meaning that either there is an extra chromosome or an excessive repetition of the same genes on a particular chromosome. In the case of Down Syndrome, ...


1

To rephrase what you already mentioned in your question: For a KEGG Module to be completed (so that an organism can perform a certain function) you need a certain set of functional units or enzymes. So to evaluate the abilities of an organism you would check its genome for the gene sequences related to the module by performing the logical operation you ...


3

At the command line: wget ftp://ftp.ensembl.org/pub/release-84/gtf/gasterosteus_aculeatus/Gasterosteus_aculeatus.BROADS1.84.gtf.gz gunzip Gasterosteus_aculeatus.BROADS1.84.gtf.gz Then in R: library(GenomicFeatures) txdb = makeTxDbFromGFF("Gasterosteus_aculeatus.BROADS1.84.gtf") hist(log10(width(unique(exons(txdb))))) # exons hist(log10(width(unique(...


1

You are correct in saying that Crick, in his Wobble Hypothesis, proposed that “the base on the third position of the codon and that on the anticodon need not be complementary”, but the “need not be” in your statement is a paraphrase of the “some” in Crick’s original statement: “It is suggested that while the standard base pairs may be used rather ...


0

Having separate male and female cones reduces self-fertilization just by the physical separation (the greater distance for pollen to travel gives pollen from a different tree a larger chance of successful fertilization). A much larger effect is from the timing of flowering, since on an individual tree the female cones will be receptive at a time when the ...


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I don't understand your hypothesis. But the number of pairwise differences between two cells assuming neutrality ($\pi$) in the two different branches in $\pi = 2 \mu L t$, where $\mu$ is the somatic nucleotide mutation rate (around $10^{-11}$ on average), $L$ is the length of the sequence of interest (eventually the whole genome). $L$ can therefore be of ...



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