Elia Mascolo
@eliamascolo.bsky.social
I love studying evolution through the lens of theoretical and computational biology. Math enthusiast and amateur jazz piano player.
https://eliamascolo.github.io/
https://eliamascolo.github.io/
What a nice article!
October 25, 2024 at 10:27 PM
What a nice article!
for their binding sites. Anyway, this is not a serious test. We'll need the code to go large-scale. It's just what I came up with given the limit of 10 jobs/day. After this limited experience with the webserver, I'm impressed! 🤯 END
May 10, 2024 at 4:25 PM
for their binding sites. Anyway, this is not a serious test. We'll need the code to go large-scale. It's just what I came up with given the limit of 10 jobs/day. After this limited experience with the webserver, I'm impressed! 🤯 END
also the others we have at least one perfect solution in 6/8 cases. I also tried with totally random DNA. As I expected it binds DNA the normal way (helices in groove) even if there's no LexA binding site. Not necessarily a "wrong" prediction given how bacterial TFs "search" 8/
May 10, 2024 at 4:25 PM
also the others we have at least one perfect solution in 6/8 cases. I also tried with totally random DNA. As I expected it binds DNA the normal way (helices in groove) even if there's no LexA binding site. Not necessarily a "wrong" prediction given how bacterial TFs "search" 8/
Case 3 is particularly convincing because the site came out quite different from the consensus. It's not the classical CTGT-n8-ACAG, but AF3 predicts that the dimer binds there. AF3 can propose more than one model, but I was only looking at the first proposed. If I consider 7/
May 10, 2024 at 4:24 PM
Case 3 is particularly convincing because the site came out quite different from the consensus. It's not the classical CTGT-n8-ACAG, but AF3 predicts that the dimer binds there. AF3 can propose more than one model, but I was only looking at the first proposed. If I consider 7/
In 8/8 cases, the TF complex is perfect, and targets DNA using correctly the DNA binding domains. In 4/8 cases, the binding occurs precisely on my "randomized" LexA sites. Uppercase: from PWM; lowercase: random; underlined red: binding expected; highlighted yellow: bound. 6/
May 10, 2024 at 4:23 PM
In 8/8 cases, the TF complex is perfect, and targets DNA using correctly the DNA binding domains. In 4/8 cases, the binding occurs precisely on my "randomized" LexA sites. Uppercase: from PWM; lowercase: random; underlined red: binding expected; highlighted yellow: bound. 6/
assembled correctly; (2) the LexA dimer contacts DNA with the known DNA binding domains in the DNA grooves; (3) it binds exactly on the "randomized" LexA sites (a pattern of 16 bp within the 40 bp). Here are the results on 8 sequences (we can't run >10 jobs/day at the moment) 5/
May 10, 2024 at 4:20 PM
assembled correctly; (2) the LexA dimer contacts DNA with the known DNA binding domains in the DNA grooves; (3) it binds exactly on the "randomized" LexA sites (a pattern of 16 bp within the 40 bp). Here are the results on 8 sequences (we can't run >10 jobs/day at the moment) 5/
at which the site starts is also random (Uniform) so that the sequence may not be in the center. I input the sequence of LexA, and set "Copies" to 2 because LexA acts as a dimer. I then try AF3 on the sequences I generated. I consider the test passed if: (1) the dimer is 4/
May 10, 2024 at 4:20 PM
at which the site starts is also random (Uniform) so that the sequence may not be in the center. I input the sequence of LexA, and set "Copies" to 2 because LexA acts as a dimer. I then try AF3 on the sequences I generated. I consider the test passed if: (1) the dimer is 4/
sites I mean that I generate the DNA sequences by picking the base at each position according to the probabilities in the position weight matrix. You can get a seq that was not even among the examples. Then I embed each site into random DNA, for a total of 40 bp. The position 3/
May 10, 2024 at 4:20 PM
sites I mean that I generate the DNA sequences by picking the base at each position according to the probabilities in the position weight matrix. You can get a seq that was not even among the examples. Then I embed each site into random DNA, for a total of 40 bp. The position 3/
of all, from what I read from Supplementary 2.5.2, AF3 was trained on Jaspar, which doesn't contain motifs for bacterial transcription factors! Please let me know if I'm missing some way in which bacterial TF motifs may have been available to AF3. Secondly, by "randomized" 2/
May 10, 2024 at 4:19 PM
of all, from what I read from Supplementary 2.5.2, AF3 was trained on Jaspar, which doesn't contain motifs for bacterial transcription factors! Please let me know if I'm missing some way in which bacterial TF motifs may have been available to AF3. Secondly, by "randomized" 2/