Genetics is the branch of biology that deals with the transmission and variation of inherited characteristics.

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What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
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90 views

Is “Fight or Flight” distance genetic

If you took a newborn animal and completely isolated it from its species, would it be capable of assuming a fight or flight distance preset by its species, due to their being no basis for what could ...
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87 views

What triggers DNA to produce proteins?

What is the trigger for DNA to produce proteins or RNA? I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses ...
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476 views

How does the modern theory of evolution solve these apparent problems? [closed]

I hold to the truth of Evolution, but I've encountered several problems with it, that I can't answer, and I can't find an answer for, despite much research. If would be great if anyone can answer ...
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395 views

When can a virus modify DNA in every cell of a living organism?

I've recently heard about experiments with brain tissue, where a virus is introduced in a rats brain, causing a "glow when electric charge is present" protein to be created. This protein then helps to ...
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325 views

How to compare SNP from genotyping results for multiple people with a known phenotype?

I'm looking at different genotyping profiles available at opensnp.org and am trying to compare profiles for people with different phenotypes. For example, given 10 profiles of people who can roll ...
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41 views

Is there are practical lower limit to gene length in E. coli?

Question is rather self-explanatory. Putting aside other post-transcriptional factors like rate of degradation of transcript, what is the smallest gene ever reported to have successfully been ...
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1answer
44 views

How diverse are dogs in their traits other than appearance?

I've asked this question about dogs not so long ago, and the short answer was - dogs are the most diverse looking species of mammals because they got a small number of genes that have a big impact on ...
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2answers
148 views

How does a new species survive without suffering inbreeding?

Just what the title states. The thought came from reading When has an organism evolved enough to be called a new species? I'm probably wrong but I understand new species happen sporadically rather ...
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439 views

What does phasing mean?

What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually ...
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167 views

Eusociality and Natural selection?

Eusociality, particularly focusing on the presence of certain altruistic sterile organisms within the social set-up creates questions as to why would the process of natural selection have favoured the ...
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3answers
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Do apes and humans share 99% of DNA or 99% of genes? What is the difference?

I made an answer on the Scifi.SE that can be read here. It is about how the characters in the story Jurassic Park might have gotten DNA for all the species shown. In my answer, I said this: Apes ...
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4answers
1k views

Are chromosomes from each parent split between gametes with equal probability (esp. in humans)?

I've recently read a little on Wikipedia about genetics, but I can't find a direct answer to this question. My rough understanding is this: Both males and females have pairs of chromosomes, one ...
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111 views

What do you call the non-Wild Type allele?

Can I have a list of suggestions, such as the mutated allele, other allele, etc. ? Are there any blatantly missing ones on my short list?
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4answers
152 views

Is there any other function of DNA?

We all know that DNA acts as a genetic molecule. Does DNA have any other function in the cell other than being a genetic material and carrier of information?
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1answer
87 views

Chromatin shearing: what is it and what are the effects of high-sensitivity?

I am reading a paper which discusses a complex (MSL-DCC) involved in dosage compensation of the drosophila X-chromosome. Descriptions of the complex's structure and function are given in the papers ...
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1answer
159 views

How do PLINK files and HapMap Phased files differ?

I know that PLINK and HapMap files show the same information, but can you give a thorough explanation of how exactly they differ.
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71 views

Transcriptionally-mediated DNA damage

I'm researching the genetics of brain cancer, and finding a huge number of mutations in voltage-gated channels. It stands to reason that some of this DNA damage is due to the DNA being transcribed ...
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1answer
356 views

What do rs id, allele coded 0 and allele coded 1 mean?

So, for a project I've been working on (different story), I've been looking at the HapMap Project, and their free online files. In their README file, they talk about how for each legend file for each ...
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1answer
154 views

Precursor miRNA and a mature miRNA

What is the main difference between a precursor miRNA and a mature miRNA? It is often the case that we have more than one precursor miRNA but only one mature miRNA. The miRNA-seq data contains only ...
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62 views

What is neutral genetic differentiation?

What is neutral genetic differentiation? Presumably it's a measure of the distance between organisms in terms of their genetics, but what does 'neutral' refer to?
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65 views

Eye color genetics

I am trying to find a model to link the phenotype eye color to its genotypes. I know that there exists a simple model from Davenport, which explains {brown,blue} eyes. Further, there is an extended ...
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2answers
115 views

Which texts are good for beginners to understand evolution on the genetic scope?

Are there good texts to study the evolution, how it works, and how mutations and changes lead to evolution of the organism ? And how does the information increase through the long time using ...
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3answers
154 views

Why are males more likely than females to have autism spectrum disorder?

The male to female ratio in autism spectrum disorder is around 4:1. However it seems ASD is not a simple X-linked disorder. Then how is it possible males are more susceptible than females, if the ...
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89 views

Sewall Wright for dunces

[This is one more post in my growing "X for dummies/idiots/morons/etc." series.] I've been enjoying Provine's The origins of theoretical population genetics for the last couple of days, but I must ...
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2answers
319 views

Transcription factor binding site located in intron

I have noticed that some TF binding sites are located in the introns of the genes. I am puzzled about whether the TF only binds to DNA in the initiation stage of transcription and will detach during ...
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33 views

Randomized experimental design in genetic experimentation.

I am struggling to find out if randomization is used in traditional genetic breeding experimentation with model organisms, especially in lab contexts? And why this should be so? This is part of a ...
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76 views

What are the allowed evolution operators (on protein encoding sequences)?

What are the evolution operators, meaning allowed actions on the DNA sequence that encodes a protein. I assume all evolution of genes is a result of duplication errors. So an answer could look ...
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120 views

Prenatal Marketing

This is for a short story idea. Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical ...
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85 views

Evolution after the development of sexual reproduction

My understanding of evolution is that genetic mutation occurs in individual members of a species, and they become a new species. Isn't a definition of species a group of genetically similar organisms ...
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133 views

Can any species be bred selectively/engineered to become as diverse looking as dogs?

I've done some research and it appears that dogs are the most diverse looking single species of mammals. The questions that interest me is - are dogs special in respect to genes/gene activation ...
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3answers
251 views

Can extinct animals be cloned?

Scientists have found mammoth blood, and are planning to clone a mammoth. How does one go from having its blood to a full blown living mammoth? Is it possible? Why does it matter if the blood is ...
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280 views

Can sexual reproduction create new genetic information?

Is there a small chance that in sexual reproduction a new allele forms in the off-spring that was not present in either of the parents, or are the alleles in the offspring always from at least one of ...
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1answer
90 views

Hardy-Weinberg applied to three alleles and stimation of allele frequencies

I have this equation: Corresponds to HW in equilibria with three alleles: $(p+q+r)^2=1$ Expanding the square results: $p^2+2pq+r^2+2pr+q^2+2qr = 1$ I need to separate homozygous and ...
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101 views

Is there any source for raw data of SNP genotype frequency?

On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares ...
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199 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
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114 views

How did the activities of protocells become inheritable?

I have learned that first a protocell came to exist and its characteristics came to be passed on by genetic material. So how come genes for all the activities come to incorporate into genetic ...
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359 views

TCGA data, and bioinformatics design questions for SNP/ mirna analysis

It's my first time posting to this forum but was looking for some help on the data aspects of this project. My tools of choice would be in python/R . Goal: I'm looking to create a disease specific ...
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3answers
844 views

Primer design for Gibson assembly

I'm trying to design a primer for Gibson assembly. My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid. I am unsure how to design my primers for ...
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3answers
880 views

Knockdown of long noncoding RNA (lncRNA) - how is it done?

I don't work at the wet lab and don't know all the details about the knockdown techniques. My question is: How lncRNA knockdown is done? For example - you have lncRNA that is functional in the ...
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1answer
328 views

What is solid-phase bridge amplification?

During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?
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4k views

What's the difference between shotgun sequencing and clone based sequencing?

What are the main differences between shotgun sequencing and clone based sequencing?
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248 views

DNA replication Okazaki fragments

I understand multiple origin bubbles; DNA polymerase only synthesizes DNA from 5' to 3' and all that. But what I don't understand is why it has to be in fragments. Yes, DNA is anti parallel, and so ...
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1answer
252 views

What is an epistasis group?

I have been trying to wrap my head around the concept of epistasis for a couple of days now, and I think I understand it, at least at a basic level, but I still don't understand some of the ways that ...
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2answers
61 views

Which X-Y chromosomes have the developmental genes for mammals?

I know that for a given mammal, half the chromosomes come from father and half from mother. This is typically denoted as x-y. I've recently read about "toolkit" genes that control how a cell develops ...
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4answers
123 views

Are there more descriptive ways of naming genes and gene interactions?

I couldn't help but notice just how non-descriptive the gene names that modern genetics is using. Currently I'm reading "The new science of Evo Devo" by Sean B. Carroll and here are some examples of ...
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235 views

Detecting Introns and Exons

I know that when RNA is transcribed from the original strand of DNA it contains introns and exons, and that the introns are spliced out of the strand to provide genetic diversity. However, what I ...
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1answer
83 views

Low complexity region and relaxed selection

I'm reading a text (Wagner, 2007) on identifying positive selection. In paper, the author says that low complexity regions are known to be associated with relaxed selection. I'm trying to understand ...
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2answers
136 views

How is gene expression estimated?

I'm reading this fantastic article on estimating body time: Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles and one ...
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1answer
109 views

What is the mechanism of regulation of PER /CRY genes?

I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate ...