Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6038639

Input and runtime details for job 6038639 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 6038639 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:35:57 CET 2018
?CopraRNA Started@ Fri Feb 16 20:19:35 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 21:35:30 CET 2018
?Post-Processing Finished@ Fri Feb 16 21:35:37 CET 2018
?Job Completed@ Fri Feb 16 21:35:51 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[txt] [svg]


heatmap

? Conserved, identified interactions for NC_000117 Chlamydia trachomatis D/UW-3/CX

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
97 0.03496 0.2959 ct_539 trxA -6.38 0.195495 87 -- 94 80 -- 87 thioredoxin  
134 0.05433 0.3262 ct_581 thrS -7.17 0.132364 52 -- 64 21 -- 33 threonine--tRNA ligase  
182 0.07944 0.3588 ct_320 nusG -7.37 0.119406 230 -- 236 81 -- 87 transcription termination/antitermination protein NusG  
101 0.03758 0.3036 ct_457 N/A -2.86 0.734073 54 -- 60 80 -- 86 transcriptional regulator  
88 0.03104 0.29 ct_766 miaA -2.38 0.813549 82 -- 88 27 -- 33 tRNA dimethylallyltransferase  
196 0.08741 0.3657 ct_698 N/A -4.23 0.486304 280 -- 292 22 -- 34 tRNA modification GTPase  
59 0.02324 0.29 ct_106 yceC -7.97 0.086897 139 -- 180 3 -- 31 tRNA pseudouridine synthase A  
125 0.05005 0.3262 ct_644 yohI -5.25 0.326074 256 -- 262 53 -- 59 tRNA-dihydrouridine synthase  
91 0.03287 0.2942 ct_674 yscC -7.61 0.105180 32 -- 46 36 -- 57 type II secretion system protein  
116 0.04833 0.3262 ct_570 gspF -8.17 0.078365 199 -- 207 80 -- 88 type II secretion system protein F  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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Feeds the job parameters to the input page to resubmit the job.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2