6,596 reputation
2943
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location Marseille, France
age 33
visits member for 1 year, 11 months
seen 14 hours ago

Elected moderator on Unix & Linux. Feel free to @ping me in chat if there's anything I can help you with.

I am a computational biologist with a background in biology, not computers. My PhD work was on gene prediction and comparative genomics but my current research is in systems biology, specifically protein-protein interaction networks.

profile for terdon on Stack Exchange, a network of free, community-driven Q&A sites


Dec
31
comment How would constantly growing nails have aided early human?
My guess is that they would work very much like the claws of other animals. Dogs for example will trim their nails by walking around outside. Dogs that live in houses need to have them cut.
Dec
31
revised Codon alignment via Python?
deleted 12 characters in body
Dec
30
answered Codon alignment via Python?
Dec
30
comment Codon alignment via Python?
I am quite familiar with it, thanks :). I did my PhD on comparative genomics and reconstructing evolutionary histories, I've done more alignments than I care to remember. You need to know whether two codons are synonymous or not in order to get the dN/dS but not necessarily to translate them, it's just an easy way to check. Anyway, using my dict suggestion this is pretty trivial. Feel free to @ping me in Biology Chat if you need more help with it.
Dec
30
comment Codon alignment via Python?
This question appears to be off-topic because it is about programming and not biology. Bioinformatics questions are on topic here if they are about the underlying concepts, you are asking a very technical issue whose answer will be code.
Dec
30
comment Codon alignment via Python?
Anyway, I would simply create a hash (a dict I believe they're called in Python) that links each amino acid to its codon. Then, once you have your alignment, read it and use the dict to translate back to the original codons inserting the gaps as you find them.
Dec
30
comment Codon alignment via Python?
You can do that easily enough from the DNA sequence, no need to translate. Just align and read the codons from the alignment. You seem to be complicating your life needlessly. That said, this is probably too computer geeky for this site and you would be better off asking on biostars.
Dec
30
comment Codon alignment via Python?
Why don't you simply align the nucleotide sequences in the first place? Just use any alignment software.
Dec
28
comment Studying the fruitfly nervous system
Please narrow this down a little, you could fill libraries with the sources of info on this little fly. What exactly are you after? Text books? Reviews? Original research? On what? Anatomy? Nervous system? Immune system? Sex determination?
Dec
27
comment Speciation and Phylogeny of Lactobacillus
Isn't that the exact same link I posted in my previous comment?
Dec
27
comment Speciation and Phylogeny of Lactobacillus
I deleted your first question since a 3 second search should give you the answer. See NCBI's taxonomy page for Lactobacillus for a list of the various species in the genus.
Dec
27
revised Speciation and Phylogeny of Lactobacillus
copy edit
Dec
26
answered How should I put a large phylogeny into a scientific paper?
Dec
20
revised Standard Classification of Disease
added 3 characters in body
Dec
20
answered Standard Classification of Disease
Dec
20
comment What is the life span of southern versus northern animals?
What makes you think there will be a difference? Animals that exist on both hemispheres will have similar habitats and, presumably, similar living conditions. Why would there be any difference at all?
Dec
19
comment Why temporal lobe is called temporal?
This question appears to be off-topic because it is about etymology, not biology.
Dec
19
comment Why temporal lobe is called temporal?
This is a very interesting question but unfortunately off topic here since it is about the etymology of an English word and has nothing really to do with biology. Voting to close (would be a perfectly good question to post on English Language & Usage though).
Dec
19
comment Autoimmunity and central tolerance
Could you clarify a bit? What do you mean by important? Most problematic? Most relevant? I assume the body you refer to is the human one?
Dec
19
comment How likely is it that Earth has millions of different species?
@Susan, actually found in many species, encoded by repetitive elements like LINES and ERVs etc but in none of them is it used to drive the expression of native protein coding genes nor does it change the fact that the flow of information is from genotype to phenotype via RNA: DNA->RNA->protein.