Questions tagged [genomics]

The study of genomes, the DNA complement of organisms.

Filter by
Sorted by
Tagged with
2 votes
1 answer
38 views

No. of genes and organismal complexity?

Why do humans contain trillions of cells arranged in many complex organs, and worms contain many less cells and less organs, but we and the worm have a similar number of genes? See for example Table 1 ...
0 votes
1 answer
34 views

Calculation for underlying genetic value of a phenotype given parents genetic values

What is the most accurate way to calculate a child's genetic predisposition to a phenotype, given both parents' genotypic predispositions? Assume trait X is 50% heritable and controlled by an ...
0 votes
2 answers
73 views

How many people need to have the same mutation of a gene in order for that gene to be seen as a feasible candidate for a disease?

I am learning about genome-wide association studies (GWAS) and I know that they are used to see whether certain SNPs are associated with a disease of interest. From everything that I have watched and ...
0 votes
1 answer
44 views

What software can be used for simulating human meiosis, taking linkage and recombination into account?

I want to study the nature of genetic variation in offspring from the same set of human parents. To this end, I would like to take two (male and female) complete genomes, generate gametes from them, ...
0 votes
1 answer
45 views

Can a gene transfer from a plasmid to a bacterial chromosome?

Plasmids are involved in providing resistance to antibiotics. So, can that gene or any other gene transfer from the plasmid to the bacterial chromosome? Is there any chance where antibiotic resistance ...
0 votes
0 answers
26 views

How does comparing shuffled proteomes to the unshuffled ones help us understand independent protein adaptation?

From 'Protein and DNA Sequence Determinants of Thermophilic Adaptation', by Konstantin B Zeldovich, Igor N Berezovsky and Eugene I Shakhnovich (Published: January 12, 2007 | https://doi.org/10.1371/...
1 vote
2 answers
123 views

How many generations does it take for the average descendant not to be genetically related to the ancestor?

Parent 1 and 2 have children. Assume infinite, randomly-mating population size. How many generations until the median descendant by lineage of parent 1 has 0 base pairs inherited from parent 1? I ...
-1 votes
2 answers
294 views

Accuracy of a particular genetics test

Consider the question - Are genetic tests accurate? I don't believe they are as the genes may not provide the complete information or maybe there are other genes responsible for a particular trait but ...
2 votes
1 answer
57 views

How to calculatie frequency of recombination between two genes based on their coordinates in ENSEMBL?

I have two genes: https://www.ncbi.nlm.nih.gov/gene/326619 and https://www.ncbi.nlm.nih.gov/gene/326620 both are mapped to chromosome 13. First is at position 23944778..23945232 second is at positions ...
2 votes
1 answer
54 views

Why is SF3B3 gene annotation missing in chm13_v2 gff3 file, and is it temporary?

In the annotation gff3 provided for CHM13 v2, I noticed that for the SF3B3 gene there's no entry with type "gene" (third column). However, transcripts and other annotations are still ...
4 votes
1 answer
196 views

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 ...
11 votes
3 answers
3k views

Are the number of base pairs in a given chromosome same between different individuals?

This is a basic question but I couldn't find an answer through a web search; hopefully this is the right place to ask. Is the number of base pairs in a particular chromosome the same in all ...
1 vote
0 answers
17 views

Are there limitations in using DNase I hypersensitive sites (DHSs) to identify candidate enhancers?

Candidate enhancer regions are often defined in studies by DHSs and/or certain chromatin marks. I was wondering if DHSs are exhaustive for identifying possible enhancer regions, and if there is any ...
0 votes
1 answer
64 views

What does ‘per DNA fragment’ mean?

In "[Genomics: A Very Short Introduction]" by John Archibald, the author discusses the DNA sequencing: In living cells, DNA rarely exists in isolation; it is typically bound tightly to ...
1 vote
2 answers
166 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 ...
0 votes
1 answer
296 views

How to identify an unknown species from its genome sequence [closed]

I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to ...
3 votes
1 answer
100 views

How can SNP arrays be used to detect deletions within a gene?

I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
1 vote
1 answer
55 views

Can CNVs have a phenotypic effect unrelated to the direct modification of transcriptional units?

I'd like to know how (or if) copy number variations can have a phenotypic effect unrelated to the direct disruption/movement/duplication of sequences for coding regions, promoters, enhancers etc. I ...
0 votes
0 answers
77 views

Why people carrying the same SNP doesn't have the same Promethease report

I'm a frequent user of Promethease to run health analysis based on MyHeritage SNP data dump. I ran two people through Promethease and both have the same SNP: ...
2 votes
0 answers
59 views

Why are bacterial genomes limited in size compared to eukaryotic ones?

I was looking at this graph that shows that the eukaryotic genome has "no size limit" whilst the bacterial one does. Unfortunately the graph has no reference but essentially the idea is that ...
1 vote
1 answer
87 views

Translating either rs number or genomic position to either a residue in the DNA or in the amino acid sequence

Studying Schizophrenia and reading some papers discussing polymorphisms in the 5HT-2A receptor gene (HTR2A). Specifically, the authors mention A-1438G, T102C, his452tyr. How does one best take ...
2 votes
1 answer
92 views

Transcript without a start codon in mouse genome?

I am looking at the mouse reference genome in combination with ensemble annotation and am finding many transcripts that have no start codon. For example, the transcript ENSMUST00000193149 at position ...
0 votes
0 answers
114 views

Can genetic material actually provide a physical description of appearance?

A bodies genetic material provides the blueprint for your appearance. Your predisposition to be tall, freckled, blue eyed and blonde are encoded from birth. However, external and environmental factors ...
1 vote
2 answers
572 views

Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?

Any comparable alternatives to linked read sequencing? I read that 10X Genomics discontinued its linked-reads technologies: Discontinuation of Linked-Reads At 10x Genomics, we are committed to ...
2 votes
1 answer
78 views

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 ...
5 votes
1 answer
491 views

Where can I find SARS-CoV-2 genome sequences for the UK?

I have downloaded and analysed the sequences of 832 complete samples from the European Nucleotide Archive but I cannot find a single one that was from the UK. I have also tried Genbank and they do not ...
5 votes
3 answers
1k views

Can one identify an organism based on its genome alone?

If one is given the complete genome of some unknown organism, would it be possible to systematically deduce what this organism looks like and behaves like without reference to anything else (ex: a ...
3 votes
3 answers
2k views

Is it possible to distinguish between coding and template strands from the sequence?

Let’s say you have the following DNA sequence fragment: 5’-ACCAGTACTTCGT-3’ 3’-TGGTCATGAAGCA-5’ Is there any way to determine which strand is the template ...
9 votes
2 answers
488 views

Tips for longer fragment size and higher purity of insect DNA

Aim In a pilot experiment I tested three different genomic DNA extraction methods on the non-model organism Pieris mannii (southern small white; Insecta, Lepidoptera, Pieridae). The goal was to ...
7 votes
2 answers
172 views

Is it possible to trace of the ancestry of a person by only using his/her genetic information?

Is it possible to trace the descent of a person only using his/her genome sequence?
-1 votes
2 answers
64 views

Can the metatranscriptomics replace the approach of functional metatranscriptomics/functional metagenomics?

While metatranscriptomics reveals information about the expression of genes and their functions too, Functional metatranscriptomics (https://www.nature.com/articles/ismej201167) allows the ...
2 votes
1 answer
84 views

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 ...
5 votes
2 answers
148 views

Are there known genome sequencing issues in E. coli?

Despite the fact that the human genome project was declared "complete" in 2001, there are even now still gaps due to difficult-to-sequence regions of the genome such as telomeres and ...
0 votes
1 answer
71 views

Why are there different gene expressions that are refered to the same gene in microarray experiments results?

I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
1 vote
0 answers
29 views

Chromosome Deletion Notation in Cancers

The cancer literature often refers to the deletion of certain sections of a chromosome (e.g. "17p del" or "Del(17p)" for the deletion of chromosome 17's p-arm.) Does this mean both ...
-4 votes
1 answer
55 views

Finding All of the Genes in a given Genome

I'm interested in finding the start position of each nucleotide in a given genome. I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout ...
-4 votes
1 answer
69 views

metaphors for explaining the role of DNA in the cell [closed]

Various metaphors are used to explain the central role of DNA in a cell to laypersons. These include blueprint, recipe, catalogue, instruction manual etc. I even heard someone describing DNA as a '...
0 votes
2 answers
180 views

What exactly is "chromosome topology"?

I've been reading a lot about Hi-C lately, and this has been bothering me. So far as I can tell from reading around, the topology is related to the conformation of the linear chromosome. This seems ...
2 votes
1 answer
47 views

Questions about Cohesin - what does the ATPase domain do, and any suggested PDBs to look at?

I've been reading about cohesin lately, and I'm confused about the head subunit interactions. I've read a few papers, and also found this nice figure from wiki that demonstrates the crux of my ...
-1 votes
1 answer
36 views

Truncated ORF3a protein of SARS-CoV2! Why? How does it formed?

Across the world so far, we have three truncated ORF3a proteins in SARS-CoV2 in India only. Can you illuminate me how does a protein (here accessory protein of SARS-COV2) generally get such nonsense ...
0 votes
1 answer
53 views

What is the copy number of a given gene in GRCh37?

sorry for the naive question, but how do I determine what the copy number is in GRCh37 for a gene with multiple CNVs? (e.g. DRD4).
2 votes
0 answers
59 views

Interpretation of Pangenome: high number of accessory genes

I performed a pangenomic analysis on a collection of 52 strains belonging to the same genus (some 5-6 different species). All the strains were isolated from the same environment: interior compartment ...
3 votes
1 answer
279 views

Is this basic gene diagram correctly labeled?

I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what ...
1 vote
2 answers
128 views

Genomic location-coordinate of RdRp of SARS-CoV2

I understand that nsp12 is the RdRp protein in the ORF1 of SARS-CoV2 genome. And nsp12 starts from the starting nucleotide base of orf1ab. Could you please tell me the exact genomic location ...
2 votes
3 answers
97 views

Which side of the DNA helix is used for describing SNPs?

In genetic research I often come across references to single-nucleotide polymorphisms (SNPs). An example is rs3184504(C;T). As far as I understand it: In this ...
0 votes
1 answer
236 views

Self-study genetics

I'm new at the field of genomics. I'm a theoretical physicist by training and now we would like to translate some of the ideas to the DNA, possibly in real genomic instances. The concrete example ...
4 votes
1 answer
3k views

What is structural RNA?

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 ...
1 vote
2 answers
7k views

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 ...
2 votes
1 answer
817 views

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 ...
1 vote
2 answers
3k views

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 ...

1
2 3 4 5 6