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

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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 ...
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3answers
90 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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2answers
1k views

Transcript(omics) terminology: cDNAs, ESTs, RNA-seq, etc

I've worked pretty frequently with genome and transcriptome data for several years now, but I'm still not 100% sure I understand the proper usage for certain terminology related to transcripts and ...
3
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1answer
31 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, ...
3
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2answers
91 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 ...
3
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1answer
39 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 ...
3
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1answer
26 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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2answers
156 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 ...
3
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0answers
55 views

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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2answers
229 views

How were the first primers made

I keep reading about how primers are useful in pcr -- they allow you to select a specific dna region. Similarly, in NGS or Sanger sequencing they give you a starting point. The primers I see are about ...
2
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2answers
124 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 ...
2
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1answer
103 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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2answers
191 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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1answer
42 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 ...
2
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1answer
33 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 ...
2
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1answer
84 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
67 views

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 ...
2
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1answer
53 views

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 ...
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2answers
92 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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0answers
31 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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0answers
14 views

Why there are two rounds of cytosine de-methylation in mammalian development?

I assume that the key biological meaning of cytosine de-methylation during germline development in germline progenitor cells is to reset imprinted genes and then set methylation pattern on these genes ...
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0answers
26 views

What is the best way to perform ultra-deep targeted sequencing of few samples?

I performed recent whole genome/exome sequencing in tumor samples and now I would like to take a few of these variants (say maximum 50 amplicons) to: 1) Validate them in the original samples 2) ...
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0answers
40 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 ...
2
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0answers
32 views

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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34 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 ...
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90 views

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 ...
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173 views

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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2answers
77 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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1answer
61 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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2answers
104 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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1answer
52 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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1answer
56 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
53 views

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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2answers
442 views

How many recombination events are there per generation in humans?

I'm looking for a reference that tells me how many recombenation events occur in humans from one generation to the next. Assuming that the human genome is a 3.3 GigaBases long DNA sequence, how many ...
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1answer
56 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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1answer
75 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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1answer
439 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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2answers
417 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 ...
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2answers
32 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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1answer
24 views

Could the proteome of E. coli be fluorescently labelled?

What proportion of the total number of proteins in E. coli could be fluorescently labelled for PALM/STORM imaging?
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1answer
49 views

What is the close and related genome used for in Gene models?

all I am a little bit confused about using the related genome or reference genome. When we have a reference genome, we can do alignment. Also we can do the assembly. Can you give some more reason ...
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39 views

Regulation of the replication of mtDNA at embryonic level

While reading an article on mitochondrial inheritance I came across this link. The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. ...
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0answers
20 views

EMBOSS matcher and supermatcher - incongruent results?

I am trying to align a sequence to the mouse genome. I know a priori that part of my sequence should align to chromosome 9, but not all of it. I gathered that EMBOSS' ...
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0answers
48 views

“Gold standard” for CNV detection methods?

Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...
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0answers
47 views

Paired-end mapping exercise

Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome. Then among libraries ...
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2answers
91 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 ...
0
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2answers
48 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 ...
0
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1answer
39 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 ...
0
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1answer
56 views

Supercomputer and undergraduates [closed]

Is it common for an undergraduate to run their thesis (evolutionary genomics) in a supercomputer? In my country, few supercomputers exist, but I'm not sure how it is for bachelors in the US or Europe. ...
0
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1answer
65 views

bioinformatics /genomics [closed]

i am looking for likely truncation sites to prove recombination in sequences. i have 4 sequences. i believe one to be the "real sequence" and the other 3 to be recombinants caused by cleavage possibly ...