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BackofenLab / IntaRNA-benchmark

Data and scripts to benchmark IntaRNA
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additional sRNAs #19

Open martin-raden opened 5 years ago

martin-raden commented 5 years ago 
"RybC"  "b0619" "dpiB/citA" "NC_000913" "Mandin:Gottesman:genet_appro_for:2009" "https://doi.org/10.1111/j.1365-2958.2009.06665.x"      "Fig6"
martin-raden commented 5 years ago 
"MicM" "ybfM" "Rasmussen:Johansen:Nielsen:conse_small_RNA:2009" "https://doi.org/10.1111/j.1365-2958.2009.06688.x"      ""
martin-raden commented 5 years ago 
"McaS"  "b1040" "csgD"  "NC_000913" "Jorgensen_Nielsen_Boysen-Small_regul_RNAs-2012"    "https://doi.org/10.1111/j.1365-2958.2012.07976.x"      "MUTATION NOT FOUND @MARTIN"
martin-raden commented 5 years ago

ChiX - chiP Fig3D in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2751969/

martin-raden commented 5 years ago

OmrAB - dgcM Fig 2 in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443205/

martin-raden commented 5 years ago

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116593

martin-raden commented 5 years ago

ChiX;b0619;dpiB/citA;NC_000913;Mandin:Gottesman:genet_appro_for:2009

chix = rybc https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2958.2009.06665.x

C55G&G-35C|G56C&C-36G|G57C&C-37G

martin-raden commented 5 years ago

ChiX;b0681;chiP;NC_000913;Rasmussen:Johansen:Nielsen:conse_small_RNA:2009

chix = micm https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2958.2009.06688.x

G55C&G-18C,C56G&C-19G

martin-raden commented 5 years ago

https://www.pnas.org/content/116/8/3042

martin-raden commented 5 years ago

https://rnajournal.cshlp.org/content/early/2013/07/26/rna.039537.113.full.pdf

martin-raden commented 5 years ago

https://www.cell.com/article/S1097-2765(14)00400-6/fulltext

martin-raden commented 5 years ago

https://www.researchgate.net/figure/Stem-loop-2-of-RcsR1-directly-interacts-with-the-5-UTR-of-sinI-A-Predicted_fig4_284277724

martin-raden commented 5 years ago

https://www.researchgate.net/figure/EcOnc01-AgvB-Acts-as-an-Anti-sRNA-to-Inhibit-GcvB-Repression-A-Interactions_fig10_262941331

martin-raden commented 5 years ago

https://www.researchgate.net/figure/Phenotypic-suppression-by-complementary-mutations-in-ydaMgfp-mRNA-and-RprA-provides_fig7_221853109

martin-raden commented 5 years ago

https://msphere.asm.org/content/4/1/e00561-18

martin-raden commented 5 years ago

http://parts.igem.org/Part:BBa_K581004

martin-raden commented 5 years ago

https://www.frontiersin.org/articles/10.3389/fmicb.2018.00763/full

martin-raden commented 5 years ago

http://parts.igem.org/Part:BBa_K581000

martin-raden commented 5 years ago

https://link.springer.com/protocol/10.1007/978-1-4939-7634-8_10

martin-raden commented 5 years ago

https://www.researchgate.net/figure/Interaction-with-oppA-mRNA-involves-both-CU-rich-regions-of-Rli22-The-interaction_fig2_305212168

martin-raden commented 5 years ago

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mmi.13857

martin-raden commented 5 years ago

GcvB Targets in E.coli https://doi.org/10.1111/mmi.14168

martin-raden commented 4 years ago

https://www.hindawi.com/journals/isrn/2012/636273/fig1/