Structures
Some knonw RNA structures are collected from all kinds of databases and papers. The conserved rRNA structures from CRW database are alse collected.
Collected structures are located in /150T/zhangqf/GenomeAnnotation/Known_Structures
| file | description | source |
|---|---|---|
| human_18S.dot | human 18S rRNA structure | RNAstrand |
| human_28S.dot | human 5.8S+28S+5S rRNA structure | Ribovision |
| human_7SK.dot | human 7SK snoRNA structure | RNAstrand |
| human_Cata_cofactor.dot | human catalase cofactor RNA structure | RNAstrand |
| human_RiboRRNA.dot | human RNase P RNA | RNAstrand |
| human_SRP.dot | human signal recognition particle RNA | RNAstrand |
| mouse_RepA.dot | mouse RepA structure | Pale's MolCell paper |
| mouse_RiboRRNA.dot | mouse RNase P RNA | RNAstrand |
| mouse_SRP.dot | mouse signal recognition particle RNA | RNAstrand |
| yeast_16S.dot | yeast 16S rRNA | RNAstrand |
| yeast_23S.dot | yeast 23S rRNA | RNAstrand |
| CRW/*.dot | human/mouse/yeast rRNAs | CRW database |
| RNAStralign/* | RNA structure datasets from Mathews lab | Mathews lab |
| ArchiveII/* | RNA structure datasets from Mathews lab | Mathews lab |
icSHAPE data of rRNA of human, mouse and yeast can be ploted with Colors.Map_rRNA_Shape in IPyRSSA
import Colors
assert sequence_18S == Colors.get_rRNA_refseq('human_small')
Map_rRNA_Shape(sequence_18S, shape_list, 'human_small', '/path/human_18S', mode='label', cutofflist=[0.3,0.5,0.7])
human signal recognition particle RNA
human RNase P RNA
