Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 3202356

Input and runtime details for job 3202356 (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 3202356 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:02 CET 2018
?Processing Started@ Fri Feb 16 15:24:35 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:03:47 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:03:55 CET 2018
?Job Completed@ Sat Feb 17 02:04:28 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

The job description you specified

GcvB


Output download complete results [zip]

Downloadable files

[csv]
[txt]
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[txt] [svg]


heatmap

? Conserved, identified interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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 0 0 stm2982 gcvA -98.53 0.000000 1 -- 73 1 -- 73 transcriptional regulator GcvA  
130 0.00652 0.1774 stm4228 malF -14.47 0.143021 162 -- 175 1 -- 15 maltose ABC transporter permease MalF  
179 0.009806 0.1951 stm3912 rep -13.00 0.240883 219 -- 287 22 -- 83 ATP-dependent DNA helicase Rep  
86 0.004005 0.1596 stm1961 fliS -19.11 0.024619 1 -- 77 23 -- 90 flagellar export chaperone FliS  
91 0.004202 0.1596 stm0387 yaiI -16.26 0.073758 5 -- 45 23 -- 58 similar to E. coli orf hypothetical protein (AAC73490.1); Blastp hit to AAC73490.1 (192 aa) 89% identity in aa 41 - 191  
103 0.005167 0.1728 stm2670 aroF -17.31 0.049328 173 -- 242 25 -- 90 3-deoxy-7-phosphoheptulonate synthase  
7 8.283e-05 0.04123 stm1953 yedO -23.64 0.004188 172 -- 228 31 -- 88 D-cysteine desulfhydrase  
8 9.263e-05 0.04123 stm0369 prpC -29.42 0.000431 202 -- 269 31 -- 91 2-methylcitrate synthase  
13 0.0002148 0.05681 stm4275 acs -17.09 0.053801 176 -- 229 31 -- 87 acetate--CoA ligase  
16 0.0002876 0.06194 stm1378 pykF -16.63 0.064116 5 -- 66 31 -- 91 pyruvate 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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Results are computed with CopraRNA version 2.1.2