6,209 reputation
2842
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location Marseille, France
age 33
visits member for 1 years, 8 months
seen 8 hours ago

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.


Mar
24
comment Clustal Omega - convert from distance into # of substitutions
What exactly do you mean by "positions" in your alignment? How many sequences are we talking about? Can you show an example of the matrix and your desired result?
Mar
24
comment Are there specific features of birds that cats/small predators are attracted to?
@shigeta they do? I would have guessed they use their echolocation.
Mar
24
comment Are there specific features of birds that cats/small predators are attracted to?
Heh, what an interesting idea! I suspect you won't succeed (though I hope I'm wrong), I think that cats are more attracted to movement than anything else. They seem to jump at anything that moves.
Mar
18
comment How can I re-format my DNA motifs' position weight matrices?
I'm not familiar with this program either but PWMs in general are always relative. What you get is a value indicating how often a particular residue is found a t a given position. Multiplying with an arbitrary value shouldn't affect the result in any way, as long as you multiple all values. Basically 1 means you always have that residue at that position. If you multiply by say 100, you can treat them as percentages. But yes, the implementations could vary depending on what you're feeding them to.
Mar
18
comment How can I re-format my DNA motifs' position weight matrices?
Yes, his solution is cleaner but I doubt there will be any difference. Remember that PWMs are relative so multiplying by anything should be fine really.
Mar
18
comment How can I re-format my DNA motifs' position weight matrices?
Why not just multiply everything by 10? The PWM will still be correct since its values are relative to each other, you just make 1.00 into 10 and 0.28 into 28 etc.
Mar
18
comment Where people age at slower pace - mountain or seashore
What makes you think there is a difference? Unless you give reasons for this assumption, your question can't be answered.
Mar
15
comment Does the lung absorb organic food?
It would also absorb inorganic food by the way, salt for example.
Mar
11
comment How do wild animals get rabies?
@dVaffection no, you're anthropomorphising, a virus doesn't "strive" to find a host any more than an Oxygen strives to find two Hydrogens to make water. We are at the frontier between life and chemistry here.
Mar
11
revised What makes the amide bond the lowest energy pathway?
Clarified title to better reflect the content of the question; edited tags
Mar
11
comment How do wild animals get rabies?
@dVaffection that one is the age old question of the chicken and the egg, not really within the scope of this site :) Anyway, many viruses can survive outside a host (for a given value of "survive") so some can be airborne and picked up by the host that way.
Mar
11
comment How do wild animals get rabies?
@dVaffection For example, ticks can carry lime disease, they're not affected by it but can still pass it on to you. Similarly mosquitoes and malaria. The latter is explained nicely in wikipedia. You can have a similar situation with viruses, that's what Chris means by "natural host".
Mar
10
comment What can thrombosis lead to?
@scaaahu this is a homework question. Masi is copying a question he presumably got in an exam and is wondering about it.
Mar
9
answered In biosynthesis of cysteine and methionine, where does the sulfur come from?
Mar
9
revised In biosynthesis of cysteine and methionine, where does the sulfur come from?
added 3 characters in body
Mar
8
revised What did Richard Feynman contribute to molecular biology?
typo
Mar
8
revised What did Richard Feynman contribute to molecular biology?
edited body
Mar
8
awarded  Nice Question
Mar
7
reviewed Close Do's and Don't's of Undergraduate Research?
Mar
7
comment Do's and Don't's of Undergraduate Research?
This is indeed off topic. However, what can you do? Learn. That's all that will be expected of you.