Questions tagged [genomics]

The study of genomes, the entire set of genes in an organism.

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74 views

Understanding conclusions that functional regions are under negative selection?

I am reading in notes for a comparative annotation lecture that : all DNA is subject to mutations most functional regions are under negative selection (ie., mutations are often deleterious) The ...
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In genome research, what is the problem in Mapping that may be caused by reads being too short?

In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back ...
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Need help distinguishing between a primary and secondary source

I am trying to figure out if the following article is a primary or secondary source. I'm leaning towards secondary but here are my cases for both. Primary: Published in a peer-reviewed journal. ...
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What does “This variant falls on 11 transcripts in 3 genes” mean in the output from GnomAD?

The gnomAD browser provides information on variants of genes (in this link, for the SAMD11 gene.) The report on a particular variant, like this one, includes the information in the header that says ...
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What is the metagenome like for other classes of animals?

Lately there's been a lot of discussion around the many non-human cells essential to a healthy human body — called the microbiome, or metagenome. Much of this is in the gut microbiome. See this ...
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Topological property of DNA

I was reading a course about DNA Supercoiling, and I stopped at this definition : [...] In the case of DNA, a topological property is one that is not affected by twisting and turning of the DNA ...
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Is DNA sequencing coverage a function of sample purity?

How is coverage affected by the purity of a sample? And can coverage for a sample be affected by other things, like the library preparation or manner in which the sample was stored?
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50 views

Calling Alterations in Exome Data

What are the main technical differences between accurately calling somatic point mutations vs copy number variation (CNV) in exome data? Side note: would you need other -omic data to accurately infer ...
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102 views

Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis. Of all the method listed on the ...
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How does one find the corresponding SNPs in the pair of chromonosmes in a FASTA file?

You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single ...
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148 views

Databases for metabolic pathways of human disease

Which databases contain the metabolic pathway of human diseases? I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.
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an umbrella term for homeolog and ohnolog?

Is there a word that refer to homologous chromosomes within a polyploid species? If I have AABB species, what is A to B? The words "homeolog" and "ohnolog" are reserved for the cases if the ...
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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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Alignment of sequenced fragments in Next Generation sequencing (sequence assembly) [closed]

The NGS (Next Generation Sequencing) involves fragmenting the DNA to be sequenced. This is followed by attachment to beads or flow cells and then a localized PCR is conducted. Modified bases are added ...
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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340 views

RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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Where can I upload non-human Genotype data?

I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype ...
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Genome-wide methylation analysis: sources of technical error?

We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, ...
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Assembly reconciliation

We have some bacterial genomes that were assembled using Spades, they were sequenced with and IonTorrent PGM. There are many assemblers and they give different results. I was interested in a tool ...
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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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Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks. Here is my running command: ...
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Is it possible to deduce facts about a person's parents just by studying his/her genome?

As an example, suppose Anne had abusive parents. Is it theoretically possible to deduce this from her genome even if she didn't inherit this quality (of being an abusive parent)?
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Genome and Proteome

Due to the dynamism of protein expression, a genome can give rise to different proteomes, but could we say that a proteome comes from different genomes?
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How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?

Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here? Binding of the triphosphate ...
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249 views

Making Cupriavidus metallidurans in laboratory? [closed]

This is probably a stupid question but would it be possible to 'make' Cupriavidus metallidurans? And if so how? I'am guessing it wouldn't be possible without the use of expensive equipment for genome ...
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Over winding vs under winding of a DNA

DNA supercoiling refers to the over- or under-winding of a DNA strand. Source : DNA supercoil When a relaxed DNA is subjected to bends, or openings of DNA, over winding or unwinding, its base ...
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874 views

Sequencing two strands of dna

My background is not genetics. 2.I am not interested in knowing how dna sequencing or genotyping is done. 3. I am interested just in the nature of the results as described here. Now coming to the ...
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How do biologists quantify “gene expression” in experiments?

I've read papers which contain statements such as "control of gene expression is critical in biological processes". How exactly does one quantify "gene expression"? Isn't gene expression an umbrella ...
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Where can I find DNA Sequence data for colon cancer

I am a computer scientist studying pattern recognition, and I am hoping to do some supervised learning on colon cancer. Unfortunately, I'm having a heck of a time finding DNA data in the following ...
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532 views

what does sequences overlap indicate

what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to ...
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Amount of Heterozygosity

How many loci in the human genome are heterozygous? How about other species? EDIT: I was wondering, considering for example the whole world population, how many of the human genes actually have two ...
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63 views

How are geneticists able to isolate gene functions?

As an example, this Scientific American article describes a known area in the dog genome that metabolizes carbohydrates. How is it that researchers are able to determine specific functions such as ...
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In marine DNA viral diversity studies, what would “paradigm of rampant mosaicism” refer to?

The recent paper in Cell Marine DNA Viral Macro- and Microdiversity from Pole to Pole describes the (huge) new Global Ocean Viromes 2.0 (GOV 2.0) dataset. In the Results and Discussion section, the ...
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91 views

What exactly does the phrase “chimerical sharing” mean in this abstract?

The Gizmodo article Australian Siblings Are Semi-Identical Twins, Some of the Rarest Humans Ever links to the new paper in NEJM Molecular Support for Heterogonesis Resulting in Sesquizygotic Twinning ...
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Can PCR duplicates have complementary sequences?

It is common when analyzing paired-end whole-genome shotgun sequencing data to check for and eliminate PCR duplicates. The reasoning is that the probability of sampling a fragment of the genome of the ...
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363 views

How to detect Single Nucleotide Variants (SNVs)?

This image is obtained from this paper. The description of this image is as follows:- DNA-sequence reads from a tumor sample are aligned to a reference genome (shown in gray). Single-nucleotide ...
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836 views

Gene configuration : Divergent vs convergent

I start reading a paper where they discuss the effect of the divergent promoter/gene and the convergent promoter/gene on the genetic expression of an organism. So I want to know what is the ...
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1answer
914 views

IC50 calculation [closed]

I am a computer science student and I'm in an internship at a genomics and biotechnologies research institute. My current task is to calculate the IC50 and the EC50 given a set of data as a table. ...
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1answer
617 views

(Genetics) Is a silencer the same as gene silencing (heterochromatin)?

Is silencer the same as gene silencing? I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a ...
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RNAs arising from intergenic regions

Which type of RNA molecule is coded for in intergenic regions? I think it must be a non-coding RNA but I'm unsure which type.
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125 views

Omics integration questions [closed]

Let's say that I have a population of Mus musculus in the lab. I divide it in a control group and a test group. The test group is constantly subjected to a stress (example: elevated UV radiation). ...
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8k views

What is splice junction pairs?

Splicing is a modification of pre mRNA when all introns are removed and exons are joined. What is a splice junction pair? It is two exons which connected together?
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156 views

DNA and gene activation

As far as the genetic content of each cell is concerned I have read to my satisfaction that all cells of a person's body except the red blood cells (with no nucleus and so no genetic message) and the ...
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2k views

Number of introns in a genome

Humans have approximately 21000 genes but they probably make more proteins than that. This has been explained by many mechanisms like alternative RNA splicing. My question is - If what we call as "...
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32 views

How are haplotype blocks different from genes?

According to Cardon et al. 2003, a haplotype block is A discrete chromosome region of high linkage disequilibrium and low haplotype diversity. It is expected that all pairs of polymorphisms ...
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319 views

What's a structural RNAs?

In genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Fungi/Saccharomyces_cerevisiae_uid128/) there are an archive .frn (nucleotide sequences of structural RNAs in fasta format), and I ...
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Pyura DNA extraction

I'm am struggling with genomic DNA extraction from different samples of Pyura chilensis; the DNA is degraded as can be seen on the gel. We've always used GeneJET Genomic DNA purification Kit (by ...
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79 views

Gene copies vs. gene paralogs - what's the difference?

I'm trying to get into the theory and practice of gene copy number variation (CNV) analysis, but there is something basic confusing me, which I couldn't yet figure out. Sorry if this is a dumb/trivial ...
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232 views

What is meant by genomic imprinting being reversible?

I'm not trying to understand the underlying molecular processes, rather understand it conceptually. This is what it says in my coursebook: "The imprint, obtained during gametogenesis, is reversible:...
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69 views

How can one calculate “probability of possessing a ‘perfect’ profile” from “typical optimal genotype frequencies”?

Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper? Paper link here