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Apr
19
comment Comparative Genomics
Relevant discussion on orthologs vs paralogs: What is the difference between orthologs, paralogs and homologs?
Apr
18
comment ncbi+ build blast_demo app
I'm voting to close this question as off-topic because it is about the compilation of a program, not biology.
Apr
18
comment ncbi+ build blast_demo app
Hi and welcome to the site. I'm afraid this is off topic here since it's about compiling blast as opposed to using it. You could try asking on Stack Overflow but I think your best bet would be biostars.org which is a Q&A site about bioinformatics. You'll get better answers if you explain what you consider to be "a lot of disk space". Also bear in mind that, if you're compiling NCBI blast, that will also include the various flavors (blastx, blastn, tblastn, tblastx, psi-blast etc) you can't expect it to be tiny.
Apr
17
comment Organisms that contain rare chemical elements
In that case, please edit your question to reflect what you're currently asking. Most of the elements you mention will be present in, basically, most organisms. Which ones are you asking about? Oh, and this article suggests that tin is an essential nutrient in humans as well. Please edit and narrow the question down to something specific that we can answer.
Apr
17
comment Organisms that contain rare chemical elements
Selenium is an essential trace nutrient, what makes you think humans don't have it? For example, we have ~22 (or 25, depending on how you count them) selenoproteins, each of which contains at least one selenocysteine amino acid which is a cysteine analog with Selenium in the place of sulfur. In fact, I would be surprised if any of these elements is not present (at least in trace amounts) in the human body. Do you have any references that support the absence of one of these?
Apr
7
comment Why reference genome is a reference?
@vajra78 it probably never will actually. These differences are irrelevant for most studies. You almost never care about individual genotypes, not unless this is a medical issue involving a specific individual. The point here is alignment and that is not affected by such small changes. Studies at the species level (looking at evolution or genetic regulation etc) rarely, if ever, need to take into account the intra-species variation.
Mar
25
comment Can bioluminescence be used for cancer or tumor detection?
Ah OK, that makes more sense. I was having trouble imagining how a promoter could be completely specific to tumor cells.
Mar
25
comment Can bioluminescence be used for cancer or tumor detection?
Huh, I stand corrected, thanks. I didn't know there were tumor-specific promoters.
Mar
25
comment Can bioluminescence be used for cancer or tumor detection?
What would a cancer specific promoter be? You could target a particular cell type, but how would you distinguish between tumorous and healthy? They have the same promoters. You could, perhaps, use promoters that are only active in proliferating cells but that limits the usefulness of the approach. More importantly, how would you detect the bioluminescence in, say, the liver?
Mar
24
comment Can silverfish climb and produce silk?
@Lefty in that case, please edit your question so the actual question being asked is clearer.
Mar
22
comment Do changes in an organism's cell modify the genetic information it uses for reproduction?
What kind of organism? Multicellular or unicellular? If the former, what cell? A random cell of a multicellular organism? A gamete?
Mar
22
comment Why is cold water more refreshing than warm water?
Ah, so you're suggesting that the difference in taste is down ti the relative concentrations of these receptors, right? OK, any ideas on why one would feel more refreshing (which, presumably, translates to more hydrating) than the other?
Mar
21
comment Why is cold water more refreshing than warm water?
Hi and welcome to the site. First of all, we expect answers here to be backed by references. That said, this does not answer my question. I am asking why cold water feels more refreshing, what is the biological method through which this feeling is expressed.
Mar
17
comment How can I align more than 2 sequences locally?
More than you might think. The NCBI blast lets you set things like e-value, gap penalty, match/mismatch scores, low complexity filtering. That's more than enough for 99% of uses.
Mar
17
comment How can I align more than 2 sequences locally?
The various web-based BLAST tools are basically a GUI for BLAST.
Mar
13
comment How did bullying arise evolutionarily?
@AliceD please never ever suggest cross-posting. We try very hard to avoid duplicating questions on multiple SE sites. If a question can fit on both sites, it should be tweaked to ask for different aspects of the issue based on each site's scope, not repeated.
Mar
2
comment How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median
@DevonRyan biostars is not part of the SE network. It is only cross-posting when posted on different Stack Exchange sites. We can hardly expect people not to poest anywhere else on the internet if they want to post here! We just want to avoid duplicating information across the SE network.
Feb
14
comment Is brain transplantation possible?
@ChrisStronks go for it, it's been reopened.
Feb
7
comment What is the meaning of dots and dashes in clustalw?
Please show us the sequences you are attempting to align. They look like low complexity regions which are very hard to align but we can't judge without seeing the originals.
Feb
4
comment All UniprotIDs of a cancer pathway
This will not give you the proteins in the pathway, you say yourself there are more than a thousand results! What you are seeing are the many, many proteins that are somehow involved in that biological process, including the various regulatory proteins. This is not the pathway itself which only has a bit over 200 proteins. Remember that GO terms are inherited so if a protein is annotated to a child term of GO:0043491 (e.g. GO:0051896, regulation of protein kinase B signaling) it will also be annotated to GO:0043491.