The study of genomes, the entire hereditary information of an organism.

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13
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235 views

Percentage of genome devoted to regulating gene expression

Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 ...
12
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4answers
354 views

Why did high A+T content create problems for the Plasmodium falciparum genome project?

The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
12
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1answer
497 views

Sequencing the genomes of polyploid organisms

I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about ...
11
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4answers
236 views

What can you tell about a person, having only their whole genome as information?

Well, the question is in the title, no explanation need.
11
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2answers
290 views

What are the limitations to current nucleotide sequencing technologies?

Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...
10
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2answers
198 views

Overlapping genetic information in eukaryotes

In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do ...
10
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2answers
179 views

Shortest strings not present in the human genome

What length are the shortest strings of DNA not present in any known person's genome, and what are they? And is there a database online by which I could find this out?
9
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2answers
245 views

Are there differences in DNA between humans of today and humans from 2000 years ago?

Are there any significant differences in our genome compared to the genes of our ancestors from 1000-2000 years ago? And if there are significant differences, do they result in significant ...
9
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2answers
4k views

What is the difference between SOLiD, 454, and Illumina next-gen sequencing?

I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in ...
8
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3answers
138 views

What are the limiting factors for gene length and number of exons?

I recently downloaded gene annotations for Homo sapiens from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have ...
8
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3answers
148 views

How is the sequenced genome of a person useful to him in practice, now?

Currently it is possible and not so expensive for a person to have his genome. This is useful in general for understanding how life works. But, in practice, how is this useful for the specific person ...
7
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1answer
259 views

Does DNA contain information beyond protein synthesis?

It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is ...
7
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2answers
117 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?
7
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1answer
79 views

Do antisense transcripts have different names than their sense strand transcripts?

I want to find which genes in the human genome can potentially be complementary to a transcript that could act as antisense transcript inhibtion? Are cis-NATs (naturally occuring anti-sense ...
7
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1answer
44 views

Which functional annotations could be useful?

Analyzing a genome, for a generic gene, which functional annotations (e.g from Gene Ontology) can help understanding its meaning/function or, at least, provide helpful informations? Annotations of ...
6
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2answers
385 views

What distinguishes “coding” and “noncoding” DNA from each other?

I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA". I'm just an interested layperson but I thought all combinations of ...
6
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3answers
371 views

How to map the Gene name to its Gene Symbol?

I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes ...
6
votes
1answer
238 views

Computational/mathematical models for predicting phenotype from genotype

Karr, Sanghvi, et al. (2012) propose a whole-cell computational model for predicting phenotype from genotype in Mycoplasma genitalium. Their model simulates myriad cell processes such as DNA ...
6
votes
1answer
201 views

What is the relative power of GWAS studies in different species?

I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more ...
6
votes
1answer
80 views

DNA methylation and genome size

Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability ...
6
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2answers
154 views

Effect of single-gene overexpression in the cell's response

Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression? If you overexpress a gene for a protein involved in signal ...
5
votes
1answer
158 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 ...
4
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1answer
174 views

Variations in Genome Sizes

Why is there wide variation in genome size amongst groups of protists, insects, amphibians and plants, but less variation within groups of mammals and reptiles?
4
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1answer
110 views

What about 23andMe's SNP test gives it such bad efficacy as a diagnostic tool?

The recent news about the FDA stopping the google backed 23andMe service selling any more kits got me thinking. I understand the company may have been selling it as a medical tool prematurely, but ...
4
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1answer
103 views

Inheritance of Huntington's disease

People with Huntington's disease have HTT genes with more than 37 copies of CAG repeat. The risk of extra copies being generated is higher during sperm formation than during ovum formation. Why is it ...
4
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1answer
380 views

What does conditional analysis of a SNP in a GWA study entail?

I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
4
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2answers
64 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 ...
4
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2answers
82 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
144 views

Can forensic DNA analysis be used to generate a visual approximation of a suspect?

In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
4
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1answer
92 views

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, ...
3
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1answer
130 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?
3
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1answer
50 views

Is copy number variation dynamic?

Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...
3
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1answer
128 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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2answers
68 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
votes
1answer
60 views

What is the potential function of ultra-conserved elements in the genome?

If selection pressure results in conservation of DNA sequences, what is the most plausible explanation for the existence of ultra-conserved elements (refs here and here) given that there hasn't been ...
3
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2answers
567 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
27 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
61 views

Activation Of Embryonic Genome

Embryonic gene activation is a process by which the embryo begins to transcribe its newly formed genome.As the embryonic gene activation occurs during early stages the paternal genome may not have any ...
3
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2answers
77 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
88 views

Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
2
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2answers
50 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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2answers
115 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 ...
2
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2answers
456 views

Difference between CDS and cDNA

What is the difference between Coding Sequences (CDS) and cDNA? Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured ...
2
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0answers
55 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 ...
2
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0answers
133 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: ...
1
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2answers
74 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 ...
1
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1answer
66 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
50 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
29 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). ...
1
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1answer
159 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 ...