Questions tagged [genomics]

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

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1answer
651 views

Which way to run BLAST?

I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways: Create a BLAST database of the ...
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409 views

What is meant by “the degree to which a gene is expressed” in an individual?

Here is an excerpt from a text that I was reading, Here is an example of microarray data. The idea is to take a group of different individuals and for each of them, you measure how much they do ...
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Assembly of metagenomic data

I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp). I have tried multiple assemblers (CLC, ...
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Results of a complete DNA sequencing - are they 100% reusable?

Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)? After that is done, it the complete genome can be stored and once the new genes (and their ...
4
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239 views

Can both the overlapping genes (in opposite strands) produce proteins?

I have recognized that both the forward and reverse transcripts from a genomic location code for protein products. Both do occur/express in the tissue of interest. In order to eliminate by chance ...
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96 views

Are the human genes' promoters all known?

It seems to be a basic question, but I couldn't find a certain answer. The human genome is known for more than a decade, and is available through several data providers as the NCBI etc. For the genes'...
4
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90 views

Why do we need two markers to measure a recombination rate?

In calculating recombination, Why is it necessary to take into account pairs of loci where one marker is heterozygous? Why is it necessary to take into account pairs of loci where both markers are ...
4
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1answer
139 views

Perplexing by the way of estimating the shared or different genes between humans and chimps

We share 98.5% genes with chimps (it means we have 98.5% same DNA sequeces ),so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred ...
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379 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
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277 views

Publicly available resources for learning metagenomics

We are starting a metagenomics project in our research group to study microbiota in the respiratory tract. Since the are no books yet about metagenomics, seems reading some reviews and online ...
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199 views

Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...
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123 views

Combining gene expression data from two species

I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
4
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1answer
56 views

Is there an association between environmental and mutational robustness?

The robustness of a genotype is the ability of this genotype to resist (always produce the same phenotype) to various parameters such as mutations and environment. The ability of a genotype to resist ...
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Realistic Application of CRISPR in Human Disorders

Human trials recently began to use the genome editing technology CRISPR to treat sickle cell anemia using edited stem cells. Sickle cell anemia is caused by a single DNA Mutation, and is also a ...
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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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215 views

What if a Point Mutation is seen in only half the coverage for its location?

I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the ...
3
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385 views

What is the genomic position of HLA-B*1502 variation?

I've searched the position and SNP ID of HLA-B*1502 variation. However, I couldn't find that where this variant exactly located on genome or HLA-B gene.
3
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1answer
150 views

Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?

Which part of a female mantises's DNA causes her to be a few times larger than a male mantis? Do other species have that part of DNA?
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2answers
2k views

In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis. I also understand cloning can be a ...
3
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1answer
592 views

How might gene clusters like the lac operon evolve?

The obvious answer for a gene cluster is gene duplication and mutation of one or both genes. But the genes in the lac operon seem not be so functionally/structurally similar (as compared to the Hox ...
3
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102 views

Microbiome Data

How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
3
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Is there any independent non-DNA based information system in the cell

The information in protein is not neccessarily independent of the genome as the information of amino-acid sequence comes directly from the genome. The process of post-translational modification may ...
3
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1answer
99 views

Why is GenBank growth slowing down?

https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are ...
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1k views

Do transposons usually jump from one chromosome to another?

If it is usual occurrence, does it mean that my one gene can change its location from one chromosome to another?
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305 views

Publicly available genotype data?

I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this: ...
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1answer
722 views

Can different bacteria strains of same species have different genomic sizes?

Can two different strains of a single species have different genomic sizes? I am not asking about plasmid. Can they have different sizes of actual chromosome?
3
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1answer
158 views

Sex biased gene expression in the X chromosome

It has been shown that the X chromosome is frequently enriched for female biased genes, and has a deficit of male biased genes. For example in this paper, and this one. However, I'm struggling to ...
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47 views

Exon skipping in mammals

I've heard from several sources that the predominant form of alternative splicing (at least in mammals) is exon skipping. However, my personal evidence is only anecdotal: I've heard it and read it, ...
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158 views

Sequence alignment scoring

The following table is from Deonier's text Computational Gene Analysis at p. 152. This is an exercise in global sequence alignment and scoring of alternative sequences. The text proposed a solution (...
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82 views

What is the genetic distance where linkage can be ignored?

I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree ...
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3answers
161 views

How much genomic variation one usually find within a given bacterial species?

If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to ...
3
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1answer
62 views

Finding confidence level of miRNA disease associations

I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence ...
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2answers
229 views

Why only heterogeneous SNVs for validation using genotyping arrays?

I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called ...
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50 views

Is mating between human and non-human primates theoretically possible?

I wonder if it is theoretically achievable to produce living offspring between a human and a non-human primate. Great apes have 24 pairs of chromosomes compared to our 23, however, it is known that a ...
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111 views

Construct picture of person's face from DNA

Would it be possible to construct a picture of a person's face from his/her DNA?
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Why are animal mitochondrial genomes so conserved and small in comparison to those of plants?

Background Levings and Brown (1989): Higher plant mitochondrial genomes are much larger and more complex than those of other organisms. They vary in size from about 200 kb in Brassica species ...
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3k views

What is pQTL and why do we need eQTL?

eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia). There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly ...
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3answers
9k views

How is the size of a gene defined?

Is there an agreed definition as to how many nucleic acid bases constitute a gene? If not, why not? I'm not sure I understand how the exact sizes of genes are defined.
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90 views

Excluding the Exon, What Does the Rest of the Genome Do?

The exon is the portion of the genome that encodes protein synthesis, if I understand correctly. But, this exon is apparently less than 5% of the genome. So, what does the rest of the genome do?
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999 views

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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2answers
716 views

How does the telomere repeat sequence vary in Eukaryotes?

Question: How does the telomeric repeating sequence vary in non-vertebrate Eukaryotes? If you know the repeating sequence of a given species I would appreciate hearing it. Background: Telomerase is ...
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2answers
225 views

Actual determination of the DNA sequence in the shotgun approach?

I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly ...
2
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1answer
455 views

Two sets of chromosome and the sequencing output

Humans have two sets of chromosomes that are not connected in each cell. Am I correct? I assume while sequencing DNA both of these sets have to be sequenced and the output have to be provided in some ...
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1answer
476 views

How can I download a gene sequence from GenBank (NCBI)? [closed]

Could you tell me the steps to find and download a gene sequence from GeneBank? I would appreciate your help.
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1answer
110 views

Are dogs affected by dwarfism?

My husband and I noticed a dog today that looked like a smaller version of a purebred Border Collie, although it didn't appear to be a puppy. It made us wonder if other animal species experience ...
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1answer
227 views

Whole genome sequence analysis software

Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, ...
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2answers
255 views

Accuracy of a particular genetics test

I am a newbie in biology and I am simply trying to discover the field of genomics. Consider the question - Are genetic tests accurate? I don't believe they are as the genes may not provide the ...
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3answers
261 views

Definition of the different DNA regions

Reading from Oshima et al. (2016): We identified 3,868 noncoding mutations including 394 located <5 Kb downstream, 1,762 intergenic, 1,621 intronic, 81 <5 Kb upstream, 7 UTR 3′, 2 UTR 5′, and ...
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343 views

Function and expression of pseudogenes

Can pseudogenes be transcribed into mRNA and translated into functional proteins, or should they be regarded as functionless mutated genes?
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79 views

Database of medically validated SNPs

I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of ...