RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure

Please fill out the submission form and click the Submit button given below. Input fields marked with a * are required.
(Load Example Data)

Input sequence*

Enter your input sequence here in either fasta format or linear sequence (without gaps). [?]

(or) Upload sequence file:
(or) Select sequence from genome database: This feature was disabled at May 31 2023

SNP details*

Enter your SNP details in the required format [?]
  • XposY, X is the wild-type nt., Y is the mutant and pos is the position
    of nt. (pos=1 for first nucleotide in a sequence)
  • In case of multiple SNPs, separate each SNP with hypen "-"
  • More than one SNP to test in a single run, provide them in seperate lines
(or) Upload SNP file:

Job options

Enter your e-mail adress if you want to receive a notification after the job has finished, and give your job any custom name.
Job name   


Select the mode of operation [?]
Mode 1 - based on global folding (RNAfold) [?]
Mode 2 - based on local folding (RNAplfold) [?]
Mode 3 - to screen putative structure-disruptive SNP [?]

Folding window

Select the size of flanking regions on either side of SNP [?]

Additional options

Parameters associated with mode 1 [?]
Measure distance   Correlation coefficient
Minimum length of the sequence interval
Cut-off for the base pair probabilities