CLOTE Computational Biology LAB

RNALOSS: Web server for RNA locally optimal secondary structure computation

Enter an RNA sequence of at most 100 nucleotides. Enter your email, indicate your operating system (for file uploads). Select option to either

(A) Paste/type an RNA sequence (with or without FASTA comment), or
(B) Upload FASTA file containing an RNA (with or without FASTA comment).
For RNA sequences of length 60 nt. or more, output will be returned by email. For each possible value of k, RNALOSS computes the number of k-locally optimal secondary structures for the input RNA, along with relative density of states and minimum free energy of a sample k-locally optimal secondary structure (see Documentation).


  1. Source code is available HERE.
  2. RNALOSS run time is O(n5), with space requirements of O(n3), so for sequences of length greater than 60, there will be a waiting time of several minutes, and the output will be sent by email. Sequences of at most 100 nucleotides are accepted in current web server.

Here are two sample RNA sequences for sample trial.

Email address: (required):

Select the type of operating system you use (required only for file upload):

Either paste in an RNA sequence or upload a FASTA format file containing a single RNA sequence.

Select the method of inputting the RNA sequence:

(A) Sequence:

(B) File:

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