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1h
answered Assuming if height was fully determined genetically, what would be the concordance between monozygotic pairs?
1h
comment TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
Yes, unfortunately you clearly don't have the raw count matrix. The only other process which could have generated matrices like that is the process of adding pseudo counts. People often add things like (sqrt(BA)) before conversion to a PWM to avoid taking the log of zero. You could see if you can work out the original BA from that. In general though I'd avoid trying to recover bad data like that. Count matrices should be integers.
10h
awarded  Citizen Patrol
12h
comment TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
Ah, sorry, my mistake. I didn't look at your numbers carefully enough. it looks like either those are already PWMs as opposed to count matrices (i.e. the values are log(count_freq/background_freq) ) or somebody has already done something strange to them. If it's the former you should have noticed some negative values. If it's latter you can try and do something like making the BA 100 and rounding them. Also it's not clear what algorithm you're talking about regularizing in that comment. Link?
15h
answered iPSC in drug discovery
15h
answered TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
15h
awarded  Commentator
15h
comment Swapping genes?
+1 as I agree in general - but the specific example of the non coding genome being thought of as junk I think is wrong. We've known there was a lot of noncoding regulatory DNA since at least the late 90s. And the ENCODE project's 'it's all functional' line was just marketing.
16h
awarded  Yearling
17h
answered Genetic mutations and new alleles
1d
answered What is a “homologous pair” of chromosomes in cross joining or cross over?
2d
revised What makes DNA sequences most different/recognizable from a biological perspective?
added 54 characters in body
2d
answered What makes DNA sequences most different/recognizable from a biological perspective?
Apr
28
awarded  Critic
Apr
28
comment Does a woman contain all the genes needed to make a man?
Also worth noting the existence of pseudoautosomal regions - "the genes other than SRY on the Y chromosome" are not all unique to men.
Apr
27
comment What did cyanobacteria gain from photosynthesis?
ATP is found in all known organisms, so there's every reason to think it would have been. Bacteria don't have mitochondria, so no, it wouldn't have been mitochondrial.
Apr
27
comment What did cyanobacteria gain from photosynthesis?
Literally everything an organism does requires energy. Photosynthesis provides an electrochemical gradient that can be used to make ATP - which is then used in many, many chemical reactions throughout the cell as an energy source. DNA synthesis requires ATP. RNA synthesis requires ATP. Protein synthesis requires ATP.
Apr
27
comment CRISPR/Cas for editing the human genome
It is true in general yes. But not in every case.
Apr
27
comment CRISPR/Cas for editing the human genome
"thousands similar to our target sites" is not true of all sites. It's true only of sites resembling repeats. Most sites in the genome can, for instance, have specific PCR primers designed against them. This would not be true if they all resembled repeats.
Apr
27
comment How significant is the genetic component of homosexual behaviour?
Be careful about the term 'environment' in these studies. In the breeders equation, which is the model used in most twin studies, "Non-shared environment" is just a miscellaneous bin used to account for all the variance not explained by the other terms. It therefore includes measurement error, developmental noise, etc etc. So even if environment as we usually think of it plays zero role, and it's all chance events during embryonic development, 'non-shared environment' will suck up that variance.