Welcome to SMERFA

This website is free and open to all users and there is no login requirement
SMERFA (Structural, Muscular and Elastic RNA Finder and Aligner) applies to process secondary and tertiary structures of RNA. It combines three key functions most desirable in modern RNA structure analysis:

1. Searching for 2D structure fragments
Efficient search for user-defined secondary structure fragments is carried out within 100,000 known RNA 2D structures collected in various sources, including bpRNA1-m, T-psi-C, RNAstralign, etc. Seven search modes provide flexibility in defining a query that combines sequence and 2D structure pattern, applying exact search or general shape matching procedure, using Elasticsearch engine and SQL queries.

2. 2D structure-based MSA
Multiple sequence alignment is based on RNA secondary structure and performs instantly. The use of pseudo-amino acid substitution matrix and MUSCLE aligner make SMERFA significantly outperform all the available alignment tools in terms of efficiency and quality of results.

3. Searching for similar 3D structures or fragments
Efficient search of 3D structures using backbone torsion angle pattern similarity. For this functionality multiple parameters are available allowing to search structures with different similarity levels using Elasticsearch and SQL queries.

4. 3D structure alignment
Pairwise structural alignment of 3D RNA structures is backbone-independent. It applies genetic metaheuristic and geometric search, both new and designed especially for SMERFA.

Funding

The project has been partially supported by grant 2016/23/B/ST6/03931 to MS from the National Science Centre, Poland.
SMERFA Server is provided By Poznan Supercomputing and Networking Center

What is new in version 2.3?

• Updated MSA for 2D structure: fixed problem with non matching brackets in consensus
• Species are manually curated to remove unnecessary entries
• Improved loading time for Elastic RNA finder start page
• Better examples

What is new in version 2.2?

• Improved effectivnes for elasticsearch
• Search RNA by species
• Asynchronous queries for 2D search

What is new in version 2.1?

• Updated MSA for 2D structure: optimized matrix, fixing pseudoknots, generating consensus
• New visualization for aligned structures - arc plot calculated on the basis of the consensus
• Multiple queues - each tool has it own dedicated queue
• Fixed issues with calculating alignment with mmCIF structures that were used to search database
• Better updates, no long wait to calculate statistics in 2D search
• Improved errors for wrong input
• Improved automatic data imports

What is new in version 2?

• Functionality allowing search of 3D structures on the basis of torsion angles similarity
• Possibility to directly send data from 2D structure search to 2D structure alignment
• Possibility to directly send data from 3D structure search to 3D structure alignment
• Removal of redundancy in 2D structure database. Structure with the same sequence and secondary structure has now one entry with multiple IDs assigned
• Added categories for 2D search
• Improved algorithm for 3D structure alignment
• Visualization of 3D structures
• Possibility to search 3D structure using mmCIF format
• Fixed issue with missing PDB entries