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

learn more… | top users | synonyms

13
votes
2answers
251 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
votes
4answers
485 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
votes
1answer
566 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
votes
4answers
264 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
votes
2answers
354 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
votes
2answers
206 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?
10
votes
2answers
220 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 ...
9
votes
2answers
269 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
votes
2answers
6k 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
votes
3answers
142 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
votes
3answers
156 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 ...
8
votes
1answer
290 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
votes
2answers
452 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 ...
7
votes
2answers
120 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
votes
3answers
131 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 ...
7
votes
1answer
83 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
votes
1answer
59 views

Are recessive, deleterious alleles less common on the X chromosome than the autosomes in humans?

As there is a potential for them to be more readily purged in hemizygous males (and in cell lineages in females with the deleterious-allele-bearing chromosome activated), I would expect the frequency ...
7
votes
1answer
46 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
votes
3answers
642 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
273 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
227 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
82 views

Why extract DNA from certain white blood cells instead of whole blood?

In my lab, human DNA is extracted from whole-blood samples. I don't actually do the extractions and I am not familiar with the specific protocol but I understand that platelets and red blood cells ...
6
votes
1answer
86 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
votes
2answers
165 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
2answers
86 views
5
votes
1answer
231 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?
5
votes
1answer
132 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 ...
5
votes
1answer
209 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
votes
2answers
326 views

What's the longest transcript known?

What's the longest functional transcript known? I'm wondering about RNA length post splicing, so not including introns.
4
votes
2answers
187 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 ...
4
votes
2answers
230 views

How many different protein coding genes are in the Human Biome?

There are approximately 20k protein-coding genes found in the human genome. This number is presumably very small when considering all the genomes found in the diverse microbes associated with the ...
4
votes
1answer
143 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
votes
1answer
738 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
votes
2answers
81 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
votes
2answers
90 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
votes
1answer
178 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
votes
1answer
94 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, ...
4
votes
1answer
31 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 ...
3
votes
1answer
134 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
votes
1answer
52 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
votes
1answer
140 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
votes
2answers
71 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
3answers
66 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: ...
3
votes
2answers
814 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
votes
1answer
26 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
votes
1answer
31 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
votes
2answers
125 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
votes
0answers
92 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
votes
2answers
76 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
votes
2answers
66 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 ...