6,761 reputation
21247
bio website
location Marseille, France
age 34
visits member for 2 years, 1 month
seen 18 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


Sep
1
awarded  Nice Answer
Aug
25
awarded  Yearling
Aug
23
comment Why was disease transfer to the Americas one-way?
I find this very hard to believe (though I know absolutely nothing about it so I am likely wrong). Surely at least the parasites were a problem for the colonists! We know there are all sorts of parasitic pathogens endemic to the Americas, none of which would be familiar to the European immune systems. Weren't they an issue?
Jul
15
comment Turning publicly available genome data into proteins
@nether that's exactly what I'm talking about. Note that i) they used M. genitalium, the simplest organism known to man, which is orders of magnitude simpler than a "white blood cell" (there's no such thing by the way, there are dozens of cell types called that) ii) they used a hell of a lot more information than the DNA sequence and iii) despite all this, the model is extremely limited. It can predict certain behaviors but cannot be considered a "true" representation of the living cell. My main point is that expecting to model a cell by using its DNA sequence is impossible.
Jul
15
comment Turning publicly available genome data into proteins
@nether ah, good, I'm glad to hear that. There is actually a lot of work being done in the subject. What is impossible (today) is to create a full working model of a cell. Impossible not because you're not good enough but because we simply don't understand the cell well enough. That could change in the future, what will never change is that the DNA sequence will never be enough for this. The sequence is only a subset of the information necessary to model a cell. By the way, you might want to look up BioPerl or BioPython if you're going to be working with this type of data.
Jul
15
comment E-value BLAST cut-off
No. We can never decide on homology based on the e-value alone and there is no single magical threshold. The threshold you choose will always depend on the particular question you are asking (how diverged are the species? How long is your sequence? How large is the database? Is this nucleotide or protein blast? etc). What is important for deciding homology is the particular regions of a sequence that are conserved (e.g. domains). For example, if you search for a homolog of a very short sequence with repetitive regions, you will never have a small e-value.
Jul
14
comment Book recommendation on mammal (or just primate) behaviour, especially in relation to child-rearing
Please don't fall into the other new age fallacy that states that natural == good. Rape is perfectly natural for example (just look at cats) as is incest (most mammals) and war (chimps for example). That something is 'natural' or the way it is done by a different primate in the wild is no indication that is is a good approach for raising the young of our species. It might be, just not always.
Jul
14
comment Turning publicly available genome data into proteins
@nether you're welcome and sorry to piss on your parade and all. I really recommend you find a biologist to collaborate with. You are greatly underestimating the complexity of the task you want to attempt. First of all, it is simply impossible with the knowledge available today. Even if it were possible though, you are looking at several years work from a team of highly qualified experts. You may be a brilliant programmer but that is not enough here. Also, you are reinventing the wheel, there are already many programs that do what you have written (identify genes and translate sequences).
Jul
14
comment Turning publicly available genome data into proteins
I think the OP meant differences between different assemblies of the same genome. For example, differences in gene coordinates between UCSC and EnsEMBL.
Jul
14
revised Turning publicly available genome data into proteins
added 2 characters in body
Jul
14
revised Turning publicly available genome data into proteins
added 456 characters in body
Jul
14
revised Turning publicly available genome data into proteins
edited tags
Jul
14
revised Turning publicly available genome data into proteins
added 456 characters in body
Jul
14
comment Turning publicly available genome data into proteins
As a general note, please don't ask multiple questions on a single post. In future, please split each question into it's own post instead. I have answered all three here since in this particular case, your questions are basically irrelevant since the main problem is a huge underestimation of the complexity of the task you are attempting. Good luck though!
Jul
14
answered Turning publicly available genome data into proteins
Jul
14
comment E-value BLAST cut-off
There is no magical threshold that defines homology! It depends completely on the specifics of your situation. There are cases where you can find true homologs and an evalue >10. Everything depends on the length of your sequences, the size of your database, the conservation of your homologs etc.
Jul
9
comment does order of genes in a chromosome matter?
That's kind of cheating though. Most cancer-causing translocations are either because their insertion causes frameshifts that disable other genes or because, as in your example, regulatory elements are left out. The modern definition of a gene tends to include its regulatory elements so here, you're not changing the order of the genes but breaking them up which is a whole different thing. I can't think of any cases where the order of the genes itself is important (in eukaryotes anyway, barring operons and the like) and would be quite interested to know of any.
Jul
5
comment What bird makes this sound?
Please edit your question and mention 1) where you heard this 2) what time of day 3) what period of the year.
Jul
5
comment Review articles for best practices in modelling cellular signaling networks?
I was about to refer you to this question when I saw that you were the one asking it! Can't think of a review off the top of my head but MSB is a good place to check: msb.embopress.org/search/….
Jul
5
comment What is the scientific name of this butterfly?
Could you give us an indication of the size of the butterfly and the time of year you saw it?