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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.

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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.
Jul
1
comment Hiding identical sequences in NCBI web interface
@WYSIWYG you mean the "partially" non-redundant database? :P
Jun
29
comment How does the Cuttlefish camouflage itself accurately despite being color-blind?
@AlanBoyd indeed but since the cuttlefish changes as a function of its environment, it must have some sort of sensory apparatus that can "see" the colors. Whether this happens at the cellular or the organismal level is another matter and what I hope this question might answer.
Jun
28
comment E-value BLAST cut-off
Thanks for the edit. Note that the wikipedia article you posted cites the same ncbi link you have in your answer which also states that "A number of tests suggest that the "BLOSUM" matrices produced by this method generally are superior to the PAM matrices for detecting biological relationships." Essentially, PAM have been replaced by BLOSUM.
Jun
27
comment E-value BLAST cut-off
Sorry but this is really not correct. As explained in the page you link to, the e-value is given by E=Kmne^λS where S is the alignment's score. Since this is a measure of (among other things) the conservation of the two sequences, the e-value includes both "conservation of the gene" and "the frequency of amino acids". Also, to my knowledge, all popular BLAST implementations (and certainly ncbi and wu-blast) use BLOSUM65 matrices, not PAM by default. In fact, I don't know of any program that uses PAM matrices by default and I can't imagine why you would want to.
Jun
11
comment What is the best file format to store gel images?
True. I'm just leery of JPG since they can easily get corrupted. Personally, I'd probably just convert the TIFFs to EPS and deal with those.
Jun
11
comment What is the best file format to store gel images?
No reason to ever use jpg. PNG is also a compressed format.
Jun
10
comment Why some neurons are tetraploid
Please don't ask multiple questions in a single post. Break them up into separate questions.