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

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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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2answers
192 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?
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257 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 ...
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82 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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1answer
218 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 ...
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4answers
407 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 ...
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0answers
142 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: ...
6
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2answers
159 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 ...
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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 ...
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261 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 ...
13
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2answers
244 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 ...
8
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3answers
151 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 ...
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250 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.
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536 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 ...
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2answers
299 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 ...
7
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2answers
119 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?
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2answers
211 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 ...
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3answers
140 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 ...