6,781 reputation
21247
bio website
location Marseille, France
age 34
visits member for 2 years, 2 months
seen 1 hour 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


Feb
24
comment basic programming and bioinformatics
I'm not at all sure that R is slower than python. Both are interpreted scripting languages. C and Java are completely different.
Feb
24
answered PAH gene mutation
Feb
24
reviewed Leave Open PAH gene mutation
Feb
22
answered Why do we exhale after we hold our breath?
Feb
20
comment Why do mammals in the wild retain the “trait” of menstruating with blood?
Yes they do, most if not all mammals menstruate. Any dog owner can confirm this for example. Please research and try to answer your question before posting here. A 5 minute search for "mammal menstruation" for example would have answered it for you. If you want to know why that does not call in predators, edit your question accordingly.
Feb
20
comment Does adding milk to cereal make it harder for our body to absorb the vitamins and minerals from the cereal?
Do not migrate this to skeptics please. You've read it where? How does this apply when you're eating say a tomato, most of which consists of water. As do 90% of all foods you eat.
Feb
20
comment Phylogenetic tree
If you just want to check something, use the whole tree, you have all the information there. Just ignore the species you don't care about.
Feb
17
comment Sequence analysis software suites
TO do what? Please explain your actual requirements.
Feb
17
answered How do you find pre-miRNAs from mature miRNA Blast output?
Feb
17
revised How do you find pre-miRNAs from mature miRNA Blast output?
edited tags
Feb
15
answered How can I fetch nucleotide sequences based on ENA accession numbers and positions?
Feb
15
comment How can I fetch nucleotide sequences based on ENA accession numbers and positions?
Could you show us a sample of the file? What's the format like? What operating system are you using? You will probably need to download each sequence and then extract the subsequence, all of which is easy enough but the details depend on how your information is formatted and the system you are using.
Feb
15
revised How can I fetch nucleotide sequences based on ENA accession numbers and positions?
nothing specific to linux here
Feb
11
comment RNA secondary structure comparison
@Superbest yes, isn't that enough? The default output of t-coffee is in clustal format, a standard and widely used format for alignments. Because of the author's self importance, I had to edit the output to remove his name before being able to view the alignment in another program. Just cause the guy likes to see his name written everywhere.
Feb
9
comment is it possible to completely reconstruct a family tree by DNA comparison alone?
@har-wradim re not completely stochastic: no it's not, that's why I said largely. As for choosing the right genome from a set, absolutely, that's a completely different proposition. However, in the OP we have to choose between siblings or mother/daughter so we don't have a set to choose from, we need to decide which hypothesis fits the data. That's what I don't think is possible but this is way out of my field so I don't pretend to know.
Feb
9
comment is it possible to completely reconstruct a family tree by DNA comparison alone?
@har-wradim how can it be modeled? It is a largely stochastic process so I don't see how you could infer my parent's genomes from mine.
Feb
9
revised What is the maximum amount of different bacteria in the drinking water in Europe?
added the table
Feb
9
comment is it possible to completely reconstruct a family tree by DNA comparison alone?
Not confident enough to post an answer but I very much doubt it. There is a large element of randomness involved, I am not simply a mixture of my parent's DNA. Processes like chromosomal crossover ensure that a significant part of my genome is original so to speak. Therefore I doubt you can reconstruct a genealogy from this information.
Feb
9
answered RNA secondary structure comparison
Feb
6
asked Which of the cell types commonly found in mammals has the greatest number of mitochondria?