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visits member for 2 years, 9 months
seen Jun 13 '13 at 13:30

Feb
27
answered What can you tell about a person, having only their whole genome as information?
Feb
24
comment What is the tRNA gene copy variation between different yeast strains?
I like @bobthejoe 's suggestion. I never intended that tRNAscan-SE would be run against an assembled genome. Depending on the size of your reads vs. the size of a typical tRNA gene, you may be able to input the reads themselves into tRNAscan-SE. If coverage of each genome is deep enough, try that de novo ass0embly. Also run the unassembled reads from each strain through tRANscan-SE - perhaps these are indeed those extra copies of the tRNA genes you're searching. Lastly, are there any gaps in an assembly where known tRNA genes are? I still think my suggestion would work.
Feb
23
answered Why do restriction enzymes tend to have an even number of bases in their recognition site?
Feb
23
comment Sequencing the genomes of polyploid organisms
I'm not sure. Sequencing is not the real problem - it is accurate genome assembly.
Feb
23
comment Questions to ask to a panel of people that will be sequenced
+1 Gergana! It is definitely a gene-by-environment interaction!. As GxEs are our forte, we'd take keen interest in the study.
Feb
23
comment Questions to ask to a panel of people that will be sequenced
Yeah, the strong reason for the selection of these traits/questions is 23andMe's desire to engage a customer base with curiosity questions - like smelling asparagus metabolites in the urine. Their (business) model is quite different from a researcher trying to convince a review panel to fund their proposal, hence my call to focus on more medically oriented phenotypes. At the same time, 23andMe has an obstacle in obtaining reliable data on one's lifestyle. I have nothing against these questions when asked via the secure 23andMe site, but better questions can be asked by Pierre's colleagues.
Feb
23
answered What is the tRNA gene copy variation between different yeast strains?
Feb
23
comment ATP cost for gene expression
Is this in bacterial or human? Transcribing a pre-mRNA and splicing are significant contributors to this energy cost calculation. Don't forget charging of tRNAs with amino acids.
Feb
23
answered Can genetically modified genes jump to bacteria in the eater's intestine?
Feb
23
comment Can genetically modified genes jump to bacteria in the eater's intestine?
A basic molecular biology textbook plus one in microbiology would be sufficient to provide the details of the mechanisms described by Amy +1.
Feb
22
answered Sequencing the genomes of polyploid organisms
Feb
22
comment Questions to ask to a panel of people that will be sequenced
I hope that the Linux gene is dominant! More likely that it is rare, and in combination with certain deletions ;)
Feb
22
answered What is the most heat-tolerant organism?
Feb
22
comment How would a plant sprout and grow in a zero gravity environment?
Agreed, links are helpful, but someone may wish to refine or rerun my query, rendering links less useful. There's enough info in my response to be helpful to this audience and I think that is the main point.
Feb
22
revised Can any other animal choke on food?
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Feb
22
awarded  Editor
Feb
22
revised Questions to ask to a panel of people that will be sequenced
added 807 characters in body
Feb
22
comment Questions to ask to a panel of people that will be sequenced
The full version of this list is long and that can bring about interview or questionnaire fatigue. Do not forget to factor in the length of time for a subject to answer all questions nor the cost of entering and analyzing those responses. Frankly, if 23andMe is asking these types of questions, you shouldn't because they will beat you to a report on the association. Deep phenotyping is critical, but direct that effort to collecting lifestyle data - like diet, sleep, exercise - which all influence the genotype-phenotype association
Feb
22
awarded  Supporter
Feb
22
answered Can any other animal choke on food?