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

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On a specific practical use of DNA editing

Consider a human male, say of age 42. This human suffers from a genetic condition. If we know exactly what is wrong, and how to fix it in the DNA, is it possible to cure him? How does this work? Is ...
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29 views

What is gene density?

As per wikipedia definition, gene density is defined as: "In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in ...
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22 views

What the gene variation detection result can tell us about a cancer [duplicate]

We do a research on a particular cancer, now we have a result of the gene variation detection . What next steps do we need to do? we don't have a clear picture about this. Can you give us some ...
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32 views

An elementary question for gene variation detection procedure in a paper

“Samples were divided into subtypes; each subtype was considered separately as a test set, using the remaining subtypes as the control. In our analysis, chromosome arms were subdivided into ...
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36 views

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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41 views

What further research can the result of gene variation detection be used for [closed]

We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
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59 views

What physical traits are derived from the Neanderthal DNA in human DNA?

Some researches had found that Human DNA has a bit of Neanderthal DNA. So they suggested there would have been crossing between Homo sapiens and Neanderthals. Now the Neanderthal looked a bit ...
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76 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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2answers
36 views

How exactly are gaps defined in genomics?

My understanding is that when sequencing a genome, "gaps" refer to fragments which were not sequencing in the sequencer. Is this correctly? What are there other meanings to the term "gap"?
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46 views

How do high-throughput/NGS sequencers calculate quality scores?

I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the ...
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18 views

Genomic distribution of tRNAs in eukaryotes

The title says it all. I'm doing a literature search trying to see what is widely known and/or well established. I've found a couple of mentions that tRNAs are dispersed throughout the entire nuclear ...
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47 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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31 views

Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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34 views

Fold enrichment of chip-seq peaks in a broadpeak file [closed]

I have a broadpeak file that I downloaded from ENCODE. How can i compute the fold enrichment of the peaks in this file_format?
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56 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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95 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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64 views

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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172 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 ...
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2answers
68 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 ...
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48 views

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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1answer
13 views

Good model for comparative genomics in relation to temperature adaptation

Can anyone suggest any highly related bacterial or parasitic species which live at very distinct temperatures, which might be a good model for comparison of genomes in regard to temperature ...
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1answer
38 views

Genome Sequencing [closed]

Is Genome sequencing used to determine the relationship between two species that are believed to have a common line of descent? How accurate is this method if so? Are there more accurate methods ...
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28 views

Walkthrough Analyzing/Processing Genotyping Data for Association Studies

I need help outlining the data analysis process of analyzing genotyping data you get back from a Next Generation Sequencing experiment. Here are the steps I currently believe you go through, but I ...
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30 views

Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
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1answer
59 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 ...
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30 views

How can a sequence be downloaded from UCSC genome browser

If I have genome coordinates is there a simple way to download the entire intervening sequence from the UCSC genome browser? I found some fancy way of using ftp but I can't figure it out.
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29 views

how to find full mitochondrial genome of plants in GenBank?

I am searching for full mitochondrial genome of a species of Malvaceae family. To be more specific, I need the genus Corchorus. ...
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128 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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31 views

A trivial question on the meaning of “relatives” in an article on horizontal gene transfer

Am I right in suggesting that by close relatives the author meant closely related species, or did he have individual organisms in mind? DETECTION OF HORIZONTAL GENE TRANSFER There are ...
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1answer
256 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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126 views

Definition of Phenotype

I'm not a biologist but, I'm trying to enter molecular biology from a perspective. I have noticed that concept of genotype is quite well defined while ...
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14 views

Are Protocadherin Gamma Cluster transcripts considered separate genes?

The PDCH@ cluster of genes share exons and are therefore isoforms of each other. However, they are considered separate genes, by both HUGO and Ensembl. A "gene" is defined as "a locus of ...
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591 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 ...
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1answer
65 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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263 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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119 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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953 views

What are the programming languages important to learn for a geneticist or bioinformatician? [closed]

I am interested in learning more about both genomics and bioinformatics, with emphasis on genomics. I was told after taking an introductory course of genomics that the programming language "R" and ...
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63 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 ...
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91 views

Punnet Square for Genotype Probabilities

I'm a computational physicist by trade, and today I was working with a student that is coding a simulation that requires the interactions of different genotypes to determine which phenotype will be ...
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1k views

What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different ...
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1answer
115 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.
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93 views

How many dinosaur genes are in a chicken genome?

I read recently that we can "work back" to a dinosaur by selectively turning off certain genes in chickens, and we were able to create a chicken with a snout instead of a beak. How many dinosaur ...
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70 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
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60 views

Mathematical modelling of omics data [closed]

I'm interested in modelling host-pathogen interactions using mathematics. I know there are good resources in Pubmed but seems I'm looking for a book or introductory reviews. My background in maths is ...
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167 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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41 views

What does a read simulator do?

There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software
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Comparative Genomics

Are orthologs and paralogs examples of conserved genes? Orthologs are the genes or DNA that is present in 2 different species, having once been present in a common ancestor. It comes about by a ...
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24 views

Solid mouse (C57BL/6) WT primers

I am trying to get a good pair (or better yet, library of pairs) of primers that give me one band in WT mice (C57BL/6). Do you know where I could find such a thing? Alternatively, I thought of just ...
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1answer
50 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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46 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 ...