#RNAbenasque Jan Gorodkin talking about read profiles for RNA-seq
November 17, 2024 at 11:04 AM
#RNAbenasque Jan Gorodkin talking about read profiles for RNA-seq
#RNABenasque SE: 95% of RNA cellular mass is rRNA & tRNA; 3% is mRNA (& pre-mRNA)
November 17, 2024 at 5:40 AM
#RNABenasque SE: 95% of RNA cellular mass is rRNA & tRNA; 3% is mRNA (& pre-mRNA)
#RNABenasque AP: Unique RNAcentral IDs URS + 10-digit hexadecimal. Species specifc IDs: URSid / NCBI taxid. GO uses RNAcentral ID for miRNAs
November 17, 2024 at 4:56 AM
#RNABenasque AP: Unique RNAcentral IDs URS + 10-digit hexadecimal. Species specifc IDs: URSid / NCBI taxid. GO uses RNAcentral ID for miRNAs
Heitsch identifies high prob helices, thresholds by max average entropy, then clusters based on relationships of helices #rnabenasque
November 17, 2024 at 11:04 AM
Heitsch identifies high prob helices, thresholds by max average entropy, then clusters based on relationships of helices #rnabenasque
Hersch method: Rnastructprofiling on github #rnabenasque
November 17, 2024 at 11:04 AM
Hersch method: Rnastructprofiling on github #rnabenasque
Need to separate pairs into helix end and stacked to match shape to rna ss models heitsch nar 2013 #rnabenasque
November 17, 2024 at 11:04 AM
Need to separate pairs into helix end and stacked to match shape to rna ss models heitsch nar 2013 #rnabenasque
CEH: Shape tells about flexibility, not accessibility #rnabenasque
November 17, 2024 at 11:04 AM
CEH: Shape tells about flexibility, not accessibility #rnabenasque
CEH: models replicates ecoli result and always improves mfe accuracy #rnabenasque
November 17, 2024 at 11:04 AM
CEH: models replicates ecoli result and always improves mfe accuracy #rnabenasque
shape doesn't rescue bad mfe structures #rnabenasque
November 17, 2024 at 11:04 AM
shape doesn't rescue bad mfe structures #rnabenasque
#rnabenasque Rolf Backoken talking about improving CLIP-seq with GraphProt
November 17, 2024 at 11:04 AM
#rnabenasque Rolf Backoken talking about improving CLIP-seq with GraphProt
#rnabenasque RB: Uses graphprot score distribution to evaluate CLIP-seq replicates. Great idea!
November 17, 2024 at 11:04 AM
#rnabenasque RB: Uses graphprot score distribution to evaluate CLIP-seq replicates. Great idea!
RB: Centre for RNA bioformatics will support German groups, but will set up @Galaxyproject server for everyone #rnabenasque
November 17, 2024 at 11:04 AM
RB: Centre for RNA bioformatics will support German groups, but will set up @Galaxyproject server for everyone #rnabenasque
BJ: How well does polar requirement of AA correlate with # of Y's in codon? -0.61 #rnabenasque
November 17, 2024 at 11:04 AM
BJ: How well does polar requirement of AA correlate with # of Y's in codon? -0.61 #rnabenasque
BJ: talking about Woese et al, PNAS 166 hypothesis that codons reflect stereo-chemical properties of AAs #rnabenasque
November 17, 2024 at 11:04 AM
BJ: talking about Woese et al, PNAS 166 hypothesis that codons reflect stereo-chemical properties of AAs #rnabenasque
BZ: If you look at correlation when considering codon usage in mRNA codon regions? Correlation improves! -0.86-9 #RNAbenasque
November 17, 2024 at 11:04 AM
BZ: If you look at correlation when considering codon usage in mRNA codon regions? Correlation improves! -0.86-9 #RNAbenasque
BZ: Claim: mRNAs and their unfolded protein are comp. (& interact) b/c of Y propensity match between AA's and their codons #RNAbenasque
November 17, 2024 at 11:04 AM
BZ: Claim: mRNAs and their unfolded protein are comp. (& interact) b/c of Y propensity match between AA's and their codons #RNAbenasque
BZ: Tests AA & nucleotide interaction propensity using PDB structures #RNAbenasque
November 17, 2024 at 11:04 AM
BZ: Tests AA & nucleotide interaction propensity using PDB structures #RNAbenasque
BZ: Could act as a neg feedback loop for translational regulation or give mRNAs chaperone function for their protein products #RNAbenasque
November 17, 2024 at 11:04 AM
BZ: Could act as a neg feedback loop for translational regulation or give mRNAs chaperone function for their protein products #RNAbenasque
BZ: A's have anti-complementary in codons, G/C/U's have positive ones. #RNAbenasque
November 17, 2024 at 11:04 AM
BZ: A's have anti-complementary in codons, G/C/U's have positive ones. #RNAbenasque
Ralf Bundschuh talking about Nucleic acid protein interactions #RNAbenasque
November 17, 2024 at 11:04 AM
Ralf Bundschuh talking about Nucleic acid protein interactions #RNAbenasque
RB: Interested in how RBP binding to mRNAs changes their structure using partition function approach #RNAbenasque
November 17, 2024 at 11:04 AM
RB: Interested in how RBP binding to mRNAs changes their structure using partition function approach #RNAbenasque
RB: Computes modified partition function for all possible binding patterns, and can calculate this in O(N^3) time! #RNAbenasque
November 17, 2024 at 11:04 AM
RB: Computes modified partition function for all possible binding patterns, and can calculate this in O(N^3) time! #RNAbenasque
RB: Structural-aware predicted Kd's correlate better with experimental ones for HuR #RNAbenasque
November 17, 2024 at 11:04 AM
RB: Structural-aware predicted Kd's correlate better with experimental ones for HuR #RNAbenasque
RB: RNA structure can induce cooperatively between RBPs (talking about work published this year in NAR) #RNAbenasque
November 17, 2024 at 11:04 AM
RB: RNA structure can induce cooperatively between RBPs (talking about work published this year in NAR) #RNAbenasque
RB: Distance dependence of structure-induced cooperatively: power-law -- not exponential, so there can be long-range effects! #RNAbenasque
November 17, 2024 at 11:04 AM
RB: Distance dependence of structure-induced cooperatively: power-law -- not exponential, so there can be long-range effects! #RNAbenasque