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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


Sep
19
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.
Sep
19
answered Did the Britons 100 years ago have different intestinal flora and fauna?
Sep
19
revised peptide MHC microarray
deleted 29 characters in body
Sep
19
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.
Sep
18
awarded  Enlightened
Sep
18
awarded  Nice Answer
Sep
17
revised How long does a mosquito take to land on a host, bite, and fly off?
added 1 character in body
Sep
16
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.
Sep
16
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
8
revised Is this a grackle with an unusually long decurved bill (Phoenix AZ, USA)
Fixed grammar
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.
Sep
1
revised Why, specifically, does each generation, on average, improve upon the design of the species rather than degrade it?
added 1 character in body
Sep
1
awarded  Enlightened
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.