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location Marseille, France
age 33
visits member for 1 year, 11 months
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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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May
4
comment Whole genome amino acid composition tool?
@Masi could you clarify how you would like the answer to be improved? Perhaps edit the question to define a specific statistical calculation you would like to see?
Apr
28
comment Modern alternatives of DNA footprinting
@canadianer ah! DNAse footprinting, OK.
Apr
28
comment Modern alternatives of DNA footprinting
Identify it as what? Guess the species of origin? Guess the individual it came from? Guess its function?
Apr
28
comment PDB file for Osteopontin (SPP1)
Is the structure known?
Apr
26
comment Sequence alignment scoring
@daniel the -4 in your score is because a T in seq1 aligned to a - in seq2 has a score of -4 in the table. The -1 is because TT has a score of -1 in the table. However, while I have actually worked with this kind of thing, I have never worked with it in depth and it was a few years ago now, I may well be wrong.
Apr
26
comment Sequence alignment scoring
@daniel in which case it is probably mistaken (my approach, not your text). Taking what you show out of context, I am simply using the score for each position. So, since T- has a score of -10 in your table, I am using that.
Apr
26
answered Sequence alignment scoring
Apr
26
comment Sequence alignment scoring
Could you explain how you get that -17? A gap costs between -2 and -10 depending on which one in the table in the OP. The score of the mismatch also changes. Where are your numbers coming from?
Apr
26
revised Sequence alignment scoring
edited tags
Apr
26
comment chimeric sequences
Do you mean chimeric sequences that are artifacts of the sequencing process or actual bona fide chimeric transcripts that are present in vivo?
Apr
25
comment psychological database with sequenced DNA records
I would be very surprised if such a thing exists. Apart from the privacy issues (OK, you can anonymize the data), there aren't to my knowledge any projects for such large scale sequencing of human samples. The closest I can think of is the 1000 genomes project but I doubt any psychological data will be included.
Apr
23
comment How to determine whether the energy of a stem-loop fold is significant or not?
A predicted stem loop of what? A nucleotide chain presumably, and most likely RNA but you need to tell us.
Apr
21
comment is there a way to do batch download for all gene pathways?
What pathways? From which database? What species?
Apr
16
comment Percentage of understood human DNA
You would need to define "understanding". This is not a book where we simply have to read the words. Each "word" can have multiple different functions and we can't say with complete certainty that we understand any of them 100%. We have a pretty good idea about a relatively large part of it but understand is a loaded word.
Apr
16
comment Regarding the relation of observed human nature with evolution and/or genetics
You will need to be way more specific than that. What behavior? Which aspect of psychology?
Apr
16
comment What is the main challenge in creating a chemical male contraceptive?
@shigeta neither men nor women have any desire to take chemical contraceptives. I don't see why that would be truer for men than for women. The only difference is that women are expected to while men aren't.
Apr
14
revised Which was the last significant event in human evolution? What's next?
Fixed minor errors
Apr
14
comment What exactly makes bananas go brown?
Ah OK, thanks. I thought you were suggesting that the oxidation of tyrosine molecules was responsible for the change of color.
Apr
13
comment What exactly makes bananas go brown?
Could you explain how tyrosine gets in there? What is it that's being oxidized? I assume you mean free tyrosine molecules and not those incorporated into protein right? If I'm missing something obvious, please point it out, biochemistry was never my strong point and I haven't worked in a wet lab since university.
Apr
13
comment Is it possible to have life in vacuum?
Define life. You can probably get viral spores that can survive and even some extremophile bacteria but in a dormant state. Would you consider something that is not interacting with its environment in any way at the moment alive?