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location Marseille, France
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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


8h
comment Finding proteins in DNA sequence
@Raghavakrishna I still don't understand what you're asking. Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. If you have a question about this, please ask a new question so you can explain it clearly and get a full answer.
9h
comment Finding proteins in DNA sequence
@Raghavakrishna what do you mean? What method? If you mean the two tools I mentioned, exonerate searches both strands by default and genewise does so if you give it the -trev flag.
2d
comment Why aren't introns found on the ends of pre-RNA?
@user137 exactly. Being an exon has nothing whatsoever to do with being a coding exon. You even have transcripts that don't code for protein at all but that contain introns regardless.
2d
comment Why aren't introns found on the ends of pre-RNA?
@user137 (and Armatus) UTRs are exons, some of them even contain introns and are spliced just like coding exons.
Sep
6
comment Degenerate Alignment Analysis
This would be much easier to answer if you gave us some more context. Presumably you are referring to sequence alignments but where did you read the term? What was it referring to?
Sep
4
comment Did Darwin ever reach the conclusion that selection will remove variation?
I don't think you can simply ignore mutation like that. Each generation may have its variation reduced by selection but novel variants will also pop up through mutation and copy errors. We'd have to take both rates (that of loss and that of gain of variation) into account to answer this.
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
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
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?
Jul
1
comment Hiding identical sequences in NCBI web interface
What's your end objective? It is trivial to download the sequences and only keep one but would that be OK for you or do you need this to happen on the web site itself? Using RefSeq will bring the duplicates down to 2 for your example but since multiple sequences exist for different strains, it will be hard to avoid them altogether from the NCBI databases. What is your end objective here? There may be better ways.