Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 8350578

Input and runtime details for job 8350578 (precomputed example)

Input Parameters

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100
? Minimal rel. cluster size0.5
? Iterative organism subset analysis (beta)no

Job ID 8350578 (server version trunk)

?Job Submitted & Queued@ Mon Oct 27 19:31:06 CET 2014
?Processing Started@ Mon Oct 27 19:31:21 CET 2014
?CopraRNA Finished & Post-Processing@ Tue Oct 28 02:37:47 CET 2014
?Post-Processing Finished@ Tue Oct 28 02:37:47 CET 2014
?Job Completed@ Tue Oct 28 02:38:19 CET 2014
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=8350578&toolName=CopraRNA ( 30 days expiry )

The job description you specified

GcvB

Output download complete results [zip]

Downloadable files

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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 sampled p-values
1 0 0 stm2982 gcvA -99.71 0.000000 1 -- 73 1 -- 73 DNA-binding transcriptional activator GcvA   0
2 4.322e-06 0.007886 stm0959 lrp -14.28 0.047768 162 -- 207 124 -- 160 leucine-responsive transcriptional regulator   0
3 2.403e-05 0.02923 stm3564 livK -16.57 0.017453 157 -- 184 65 -- 90 high-affinity branched-chain amino acid ABC transporter leucine-binding protein LivL   0
4 4.264e-05 0.0389 stm4398 cycA -18.11 0.008834 177 -- 210 122 -- 161 D-alanine/D-serine/glycine permease   0
5 5.506e-05 0.04018 stm3909 ilvC -20.80 0.002725 166 -- 187 67 -- 89 ketol-acid reductoisomerase   0
6 0.0001005 0.0611 stm1299 gdhA -15.01 0.034727 136 -- 171 63 -- 91 glutamate dehydrogenase   0
7 0.0001271 0.06623 stm0680 asnB -17.38 0.012231 158 -- 182 72 -- 90 asparagine synthetase   0
8 0.0002506 0.1143 stm3523 glpR -15.19 0.032040 207 -- 224 72 -- 89 DNA-binding transcriptional repressor GlpR   1
9 0.0003207 0.13 stm3630 dppA -18.33 0.008048 158 -- 194 57 -- 92 dipeptide ABC transporter substrate-binding protein DppA   0
10 0.0004745 0.1686 stm2496 yfgE -13.93 0.055578 227 -- 243 72 -- 88 DnaA regulatory inactivator Hda   0

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

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Results are computed with CopraRNA version 2.0.1