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
?Processing 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:80/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

The job description you specified

IhtA


Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
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[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
1 6.997e-05 0.03358 ct_198 oppA_3 -8.59 0.062291 189 -- 206 17 -- 33 oligopeptide ABC transporter substrate-binding protein  
2 8.171e-05 0.03358 ct_802 rs18 -7.95 0.088258 66 -- 79 21 -- 34 30S ribosomal protein S18  
3 0.0003482 0.07439 ct_023 prfA -10.22 0.024627 158 -- 204 18 -- 56 peptide chain release factor  
4 0.0004436 0.07439 ct_864 xerD -16.31 0.000480 24 -- 38 17 -- 31 site-specific tyrosine recombinase XerD  
5 0.0004969 0.07439 ct_056 N/A -17.69 0.000175 196 -- 255 6 -- 56    
6 0.000543 0.07439 ct_280 nqr4 -8.45 0.067322 89 -- 131 2 -- 35 Na(+)-translocating NADH-quinone reductase subunit D  
7 0.0007305 0.07962 ct_505 gapA -11.17 0.013986 23 -- 47 19 -- 39 glyceraldehyde-3-phosphate dehydrogenase  
8 0.0008373 0.07962 ct_066 N/A -11.14 0.014316 190 -- 205 17 -- 33    
9 0.0008717 0.07962 ct_743 hctA -7.87 0.092034 214 -- 220 82 -- 88 histone H1-like protein  
10 0.001873 0.154 ct_367 aroL -15.55 0.000817 132 -- 208 3 -- 59 shikimate kinase  

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