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visits member for 1 year, 10 months
seen Aug 19 at 15:04

I'm a bioinformatician with a background in evolutionary biology (mostly phylogeny).


Aug
19
comment How do I perform recurring pattern mining or regular expressions of nucleotide sequences?
For python, the Bio.motifs package from BioPython could be useful: biopython.org/DIST/docs/tutorial/Tutorial.html#sec244
Dec
5
comment Cats, Dogs and Bears - how are they related?
What do you mean by "paralogous clade"?
Oct
25
comment Family tree for edible plants?
Beware that tolweb is not very accurate: from what I understood, they lack the funding necessary to update it. So it doesn't reflect the state of the art in terms of phylogeny.
Sep
12
comment Molecular Evolution: Mrbayes never stops?
And if all what kmm suggests fail, it may be time to fiddle with finer tunings, such as concerning the proposals that are used to modify the Markov chain.
Sep
3
comment Could be an union/synergy between Math, Computer Science and Marine Biology?
I have the intuitive feeling that it may be easier to specialize in computer sciences and then apply this to marine biology than specialize in marine biology and then learn the computational tools. It may be easier to learn the tricky technical aspects with a younger brain, and later acquire the necessary knowledge to apply your technical skills to marine biology. Of course, it would be better if you could study both at the same time, but it may be difficult to arrange this.
Aug
13
comment Plant identification?
It would help if you provided more photos, such as a detail of the flower (where petals and other structural elements can be counted), the stem, the leaves, etc.
Jun
20
comment What do rs id, allele coded 0 and allele coded 1 mean?
@Alan Boyd Yes, I should have read the page further. So there is this "GRC human genome (build 37)" which is an artificial haploid reference. Is this the reference for all registered SNP? It could be but I have no certainty. One reason for my doubts is the following: Can it happen that a new SNP is identified in a portion of the genome not yet present in this reference genome? I suspect this is becoming rare, but when this reference was in earlier stages of construction, may be it could have happened.
Jun
20
comment What do rs id, allele coded 0 and allele coded 1 mean?
@terdon is the reference genome the same for every registered SNP? I mean, if you took the 0 allele at every SNP registered with a rsID, would you end up with the genetic profile of one specific individual? It seems not: I read in en.wikipedia.org/wiki/Reference_genome that "the Genome Reference Consortium human genome (build 37) is derived from thirteen anonymous volunteers from Buffalo, New York". Is that the genome used as a reference for 0/1 labelling of SNPs? And what to do when there is polymorphism in this group of people? Maybe I could make a new question...
Jun
3
comment What is this insect?
I agree it must be a Tipulidae. I also call them "cousins" in French, or "tipules". I think their larvae live in the soil, not in stagnant water. I'd bet their abundance could be related to the anormally long "winter".
May
29
comment What kind of tree could this be?
I noticed that in japanese animation, the fish are often identifiable, at least at the genus or family level. So the question makes sense to me.
May
3
comment Do immortal organisms exist?
I find your distinction between internal and external factors a bit arbitrary. What is your motivation for excluding bacterial infections as external cause of death? You might be interested in what happens in plants. Here is an example, where the plants get cloned and seem to be able to do this for an indefinite amount of time, but they loose their fertility: wired.com/wiredscience/2010/08/aspen-immortality
Apr
9
comment What's the Evolutionary Purpose of Religion?
In my opinion, social evolution is a continuation of biological evolution. In that sense, the question might be considered legitimate here.
Feb
22
comment Human evolution: Where *exactly* did the first human come from, whose parents were not?
There are cases of abrupt speciation, I think, when chromosomes are duplicated in a hybrid that would otherwise not be able to reproduce sexually. The duplication restores the ability to form viable gametes (the chromosomes can now form pairs during meiosis: en.wikipedia.org/wiki/Meiosis#Prophase_I). This is documented in plants, where vegetative reproduction allows survival of a sterile hybrid population until chromosome duplication occurs.
Feb
21
comment What species of bird is on this coin?
I know a professional ichthyologist who once had to propose an identification for a fish painted on a cave wall. Surely it is more difficult than identifying from a real specimen, a photo or a scientific drawing, but in some case, artistic representations have a precise biological source of inspiration, and it is meaningful to try identifying it. If we didn't already knew what species of bird is represented here: en.wikipedia.org/wiki/… I think it would make sense trying a identification.
Nov
27
comment Are genes associated with obesity selected for?
I would think that genes favouring obesity nowadays in contexts of constant food abundance were in the past useful to store extra nutrients, when the food availability was irregular. One day you get something, you eat as much as you can of it and store the extra in the form of fat, and then you starve for some days, living on the fat you stored on the good day. I think I heard or read about such theories, but I have no reference for it.