6,761 reputation
21247
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location Marseille, France
age 34
visits member for 2 years, 1 month
seen 10 hours 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


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
2
awarded  Curious
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 Essentially, PAM have been replaced by BLOSUM.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
revised E-value BLAST cut-off
added 307 characters in body
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
27
answered E-value BLAST cut-off
Jun
25
reviewed Reviewed Weinman AIF and High temporal resolution AIF difference
Jun
25
awarded  Notable Question
Jun
12
revised The probability of indirect human fertilization?
It was just pointed out to me that my answer was the same as yours so I included some of the quotes from mine here and deleted it.
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.
May
28
comment downloading a reference genome for alignment
Yes, NCBI is fine. So is genome.ucsc.edu or ensembl.org or genomes online.
May
23
revised Were there any flying dinosaurs?
Pretty sure there aren't any today :)
May
20
comment Is there a correlation between brain size and amount of sleep?
@MadScientist not sure, they're complaining about the cross-posting over there too and neither one has an answer. I'm not sure which site is a better fit. Darko, could you please modify your question to fit the different communities more specifically?
May
20
revised Is there a correlation between brain size and amount of sleep?
typo
May
16
answered Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment