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
131 0.05291 0.3262 ct_842 pnp -7.97 0.086989 198 -- 205 17 -- 24 polyribonucleotide nucleotidyltransferase  
2 8.171e-05 0.03358 ct_802 rs18 -7.95 0.088258 66 -- 79 21 -- 34 30S ribosomal protein S18  
9 0.0008717 0.07962 ct_743 hctA -7.87 0.092034 214 -- 220 82 -- 88 histone H1-like protein  
33 0.01042 0.2518 ct_780 N/A -7.85 0.092931 30 -- 50 15 -- 34    
102 0.03801 0.3036 ct_001 N/A -7.82 0.094515 254 -- 277 28 -- 49    
112 0.04461 0.3262 ct_089 lcrE -7.82 0.094118 129 -- 157 3 -- 33 low calcium response protein E  
39 0.01357 0.2859 ct_401 gltT -7.80 0.095127 36 -- 47 44 -- 55 sodium:dicarboxylate symport protein  
127 0.0509 0.3262 ct_808 cafE -7.80 0.095102 169 -- 204 18 -- 57 ribonuclease E  
133 0.05414 0.3262 ct_059 fer -7.78 0.096344 200 -- 207 80 -- 87 ferredoxin  
175 0.07342 0.3448 ct_738 yycJ -7.78 0.096435 160 -- 204 18 -- 50 Zn-dependent hydrolase  

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