Publications - Supplemental material
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BIOINF 16-001: Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.
Annotation files
Genomic coordinates of the different annnotation sets as gff files referring to the Yersinia pseudotuberculosis genome (NC_010465 and plasmid NC_006153; YPIII [fasta]).
File | Description |
---|---|
ncRNA.gff | Non-coding RNAs |
cdRNA_chr.gff | Coding RNAs |
5UTR_p30.gff | 5'-UTR regions extended by 30nt downstream |
ICR_m100_p30.gff | Intercistronic regions extended by 100nt upstream and 30nt downstream |
1stORF.gff | First open reading frames |
pYV_cdr.gff | Coding RNAs (plasmid) |
pYV_icr_m100_p30.gff | Intercistronic regions (plasmid) |
pYV_operons.gff | Operons RNAs (plasmid) |
pYV_UTR_p30.gff | 5UTR regions (plasmid) |
PARS Scores
The calculated PARS scores from in vitro structure probing for the annotated regions at the different temperatures 25C, 37C, and 42C.
We provide one file per annotation and temperature. Each line reports the PARS scores for one annotated region in the corresponding gff. Each line starts with the region name, followed by the scores from first to last position (in 5'-3' orientation). The entries of each line are tab-separated (tsv files).
File | Annotation set at temperature |
---|---|
ncRNA-pars-BC_05_06.tsv | Non-coding RNAs at 25C |
ncRNA-pars-BC_07_08.tsv | Non-coding RNAs at 37C |
ncRNA-pars-BC_09_10.tsv | Non-coding RNAs at 42C |
cdRNA-pars-BC_05_06.tsv | Coding RNAs at 25C |
cdRNA-pars-BC_07_08.tsv | Coding RNAs at 37C |
cdRNA-pars-BC_09_10.tsv | Coding RNAs at 42C |
5UTR_p30-pars-BC_05_06.tsv | 5UTRs (+30nt) at 25C |
5UTR_p30-pars-BC_07_08.tsv | 5UTRs (+30nt) at 37C |
5UTR_p30-pars-BC_09_10.tsv | 5UTRs (+30nt) at 42C |
ICR_m100_p30-pars-BC_05_06.tsv | ICRs (-100nt; +30nt) at 25C |
ICR_m100_p30-pars-BC_07_08.tsv | ICRs (-100nt; +30nt) at 37C |
ICR_m100_p30-pars-BC_09_10.tsv | ICRs (-100nt; +30nt) at 42C |
1stORF-pars-BC_05_06.tsv | First ORFs at 25C |
1stORF-pars-BC_07_08.tsv | First ORFs at 37C |
1stORF-pars-BC_09_10.tsv | First ORFs at 42C |
pYV_cdr-pars-BC_05_06.tsv | Coding RNAs (plasmid) at 25C |
pYV_cdr-pars-BC_07_08.tsv | Coding RNAs (plasmid) at 37C |
pYV_cdr-pars-BC_09_10.tsv | Coding RNAs (plasmid) at 42C |
pYV_icr_m100_p30-pars-BC_05_06.tsv | Intercistronic regions (plasmid) at 25C |
pYV_icr_m100_p30-pars-BC_07_08.tsv | Intercistronic regions (plasmid) at 37C |
pYV_icr_m100_p30-pars-BC_09_10.tsv | Intercistronic regions (plasmid) at 42C |
pYV_operons-pars-BC_05_06.tsv | Operons (plasmid) at 25C |
pYV_operons-pars-BC_07_08.tsv | Operons (plasmid) at 37C |
pYV_operons-pars-BC_09_10.tsv | Operons (plasmid) at 42C |
pYV_UTR_p30-pars-BC_05_06.tsv | 5' UTRs (plasmid) at 25C |
pYV_UTR_p30-pars-BC_07_08.tsv | 5' UTRs (plasmid) at 37C |
pYV_UTR_p30-pars-BC_09_10.tsv | 5' UTRs (plasmid) at 42C |
PARS-guided Predictions of Ensembles and Structures
Predicted secondary structure ensembles of all sequences (length<=400) of the annotation sets. The thermodynamic predictions are guided by the empirically derived PARS scores (applying RNAfold of the Vienna RNA package with the soft-constraint folding method of Washietl et al.). Foreach annotation set and temperature, we provide a zip archive containing 1) the predicted dot plots as postscript files and 2) the mfe secondary structure and ensemble description as text files.
File | Annotation set at temperature |
---|---|
ncRNA-BC_05_06.zip | Non-coding RNAs at 25C |
ncRNA-BC_07_08.zip | Non-coding RNAs at 37C |
ncRNA-BC_09_10.zip | Non-coding RNAs at 42C |
cdRNA-BC_05_06.zip | Coding RNAs at 25C |
cdRNA-BC_07_08.zip | Coding RNAs at 37C |
cdRNA-BC_09_10.zip | Coding RNAs at 42C |
5UTR_p30-BC_05_06.zip | 5UTRs (+30nt) at 25C |
5UTR_p30-BC_07_08.zip | 5UTRs (+30nt) at 37C |
5UTR_p30-BC_09_10.zip | 5UTRs (+30nt) at 42C |
ICR_m100_p30-BC_05_06.zip | ICRs (-100nt; +30nt) at 25C |
ICR_m100_p30-BC_07_08.zip | ICRs (-100nt; +30nt) at 37C |
ICR_m100_p30-BC_09_10.zip | ICRs (-100nt; +30nt) at 42C |
1stORF-BC_05_06.zip | First ORFs at 25C |
1stORF-BC_07_08.zip | First ORFs at 37C |
1stORF-BC_09_10.zip | First ORFs at 42C |
pYV_cdr-BC_05_06.zip | Coding RNAs (plasmid) at 25C |
pYV_cdr-BC_07_08.zip | Coding RNAs (plasmid) at 37C |
pYV_cdr-BC_09_10.zip | Coding RNAs (plasmid) at 42C |
pYV_icr_m100_p30-BC_05_06.zip | Intercistronic regions (plasmid) at 25C |
pYV_icr_m100_p30-BC_07_08.zip | Intercistronic regions (plasmid) at 37C |
pYV_icr_m100_p30-BC_09_10.zip | Intercistronic regions (plasmid) at 42C |
pYV_operons-BC_05_06.zip | Operons (plasmid) at 25C |
pYV_operons-BC_07_08.zip | Operons (plasmid) at 37C |
pYV_operons-BC_09_10.zip | Operons (plasmid) at 42C |
pYV_UTR_p30-BC_05_06.zip | 5' UTRs (plasmid) at 25C |
pYV_UTR_p30-BC_07_08.zip | 5' UTRs (plasmid) at 37C |
pYV_UTR_p30-BC_09_10.zip | 5' UTRs (plasmid) at 42C |
Raw sequence data
Raw sequence data from the experiments BC_05,...,BC_10 as fastq.gz files.
File | Description |
---|---|
BC_05.fastq.gz | S1 digest (single stranded) at 25C |
BC_06.fastq.gz | V1 digest (double stranded) at 25C |
BC_07.fastq.gz | S1 digest (single stranded) at 37C |
BC_08.fastq.gz | V1 digest (double stranded) at 37C |
BC_09.fastq.gz | S1 digest (single stranded) at 42C |
BC_10.fastq.gz | V1 digest (double stranded) at 42C |