Part Ⅰ: Data API URL Form

https://www.rna-society.org/virbase/php/api.php?keyword=*&type=*&organism=*&method=*&score=*&partial=*

  • keyword = The Gene Symbol or miRBase ID that the user wants to search
  • type = The interaction type that the user wants to search
  • organism = The organism that the user wants to search
  • method = The detection method that the user wants to search
  • score = The score interval that the user wants to limit (separate by ',')
  • partial = The search type that the user wants to limit

Specification of Tag Values

  • For " type " tag:
Valid Value Note
0 Host-Host interactions
1 Host-Virus interactions
2 Virus-Host interactions
3 Virus-Virus interactions
* don't limit interaction type

  • For " organism " tag:
Valid Value Note
Homo sapiens organism limit to 'Homo sapiens'
Mus musculus organism limit to 'Mus musculus'
* don't limit organism

  • For " method " tag:
Valid Value Note
strong the detected method is strong evidence
weak the detected method is weak evidence
prediction the detected method is prediction
* don't limit method

  • For " score " tag:
Valid Value Note
0,1 the score ranges from 0.0 to 1.0
0.3,0.7 the score ranges from 0.3 to 0.7
a,b the score ranges from a to b

  • For " partial " tag:
Valid Value Note
true exact search
false partial search
* don't limit partial

Note


Example


Part Ⅱ: IntaRNA API URL Form

https://www.rna-society.org/virbase/php/api.php?cate=1&querySeq=*&targetSeq=*&outNumber=*&outOverlap=*&outMaxE=*& outDeltaE=*&seedBP=*&seedMaxUP=*&seedMaxE=*&seedMinPu=*&seedQRange=*&seedTRange=*&temperature=*&qAccW=*& qAccL=*&tAccW=*&tAccL=*

  • querySeq = Query ncRNA (short) in FASTA, please replace "\n" with "%0A"
  • targetSeq = Target RNA (long) in FASTA, please replace "\n" with "%0A"
  • outNumber = Maximal number of (sub)optimal interactions that are predicted per RNA pair. Input value has to be parsable as Integer. The value must be greater than or equal to 1 and must be smaller than or equal to 100. Defaults to (1)
  • outOverlap = Defines where overlapping interactions in the suboptimal output are allowed: N - no overlaps at all, T - overlaps in target only, Q - overlaps in query only, B - overlaps in both query and target. Defaults to (Q)
  • outMaxE = Output only interactions with an energy below or equal to this energy in kcal/mol. Input value has to be parsable as Double. The value must be smaller than or equal to 0. Defaults to (0)
  • outDeltaE = Output only interactions with an energy below or equal to the minimum free energy (mfe) + this delta energy term in kcal/mol. Input value has to be parsable as Double. The value must be greater than or equal to 0 and must be smaller than or equal to 100. Defaults to (100)
  • seedBP = Minimal number of intermolecular base pairs in the seed region.Input value has to be parsable as Integer. The value must be greater than or equal to 2 and must be smaller than or equal to 12. Has to be greater than the number of unpaired bases within the seed (for webserver use). Defaults to (7)
  • seedMaxUP = Maximal number of unpaired bases in the seed region in both sequences. Input value has to be parsable as Integer. The value must be greater than or equal to 0 and must be smaller than or equal to 20. Defaults to (0)
  • seedMaxE = Maximal overall interaction energy of the seed interaction to be considered for further interaction prediction. The value must be greater than or equal to -999 and must be smaller than or equal to 999. Defaults to (0)
  • seedMinPu = Maximal overall interaction energy of the seed interaction to be considered for further interaction prediction. Input value has to be parsable as Double. The value must be greater than or equal to -999 and must be smaller than or equal to 999. Defaults to (0)
  • seedQRange = Seed search and position is constrained to this region of the query ncRNA. Has to be in the format 'FROM-TO' to give the coordinates FROM where TO where the seed is to be found (index counting starts with 1). Defaults to ()
  • seedTRange = Seed search and position is constrained to this region of the target RNA. Has to be in the format 'FROM-TO' to give the coordinates FROM where TO where the seed is to be found (index counting starts with 1). Defaults to ()
  • temperature = Temperature in degrees Celsius used to rescale energy parameters. Input value has to be parsable as Double. The value must be greater than 0. Defaults to (37.0)
  • qAccW = Size of the averaging window in the local query ncRNA folding (RNAplfold -W) for the computation of accessibilities. Input value has to be parsable as Integer. The value must be greater than or equal to 0. The window size has to be at least as large as the maximal basepair distance. Defaults to (150)
  • qAccL = Maximal distance of two paired bases in the local query ncRNA folding (RNAplfold -L) for computation of accessibilities. Input value has to be parsable as Integer. The value must be greater than or equal to 0. Defaults to (100)
  • tAccW = Size of the averaging window in the local target RNA folding (RNAplfold -W) for the computation of accessibilities. The value must be greater than or equal to 0. The window size has to be at least as large as the maximal basepair distance. Defaults to (150)
  • tAccW = Maximal distance of two paired bases in the local target RNA folding (RNAplfold -L) for computation of accessibilities. Input value has to be parsable as Integer. The value must be greater than or equal to 0. Defaults to (100)

Example


Part Ⅲ: PRIdictor API URL Form

https://www.rna-society.org/virbase/php/api.php?cate=2&selectSeq=*&proSeq=*&rnaSeq=*

  • selectSeq = Confirm whether to input protein sequence and/or RNA sequence
  • proSeq = Protein sequence
  • rnaSeq = RNA sequence of >= 5 nucleotides

Specification of Tag Values

  • For " selectSeq " tag:
Valid Value Note
1 Protein sequence and RNA sequence
2 Protein sequence
3 RNA sequence

Example