Download
LoopMatcher is a bioinformatics tool that searches for hairpin structures in cDNA / mRNA sequences (in FASTA, GenBank or Vienna format) with specific consensus sequences in the loop. It uses RNAfold to predict sequence structure and UShuffle to generate random sequences with a defined k nucleotide frequency. Also, sequences in GenBank format can be downloaded directly from NCBI using the NCBI access ID.
Requirements
JAVA Runtime 8. It's highly recommended to have a multicore processor to process large sequences.
* Currently, this version only runs in Windows x64.
Features
- Support to GenBank, FASTA and Vienna format files
- Process one or multiple files
- Get and process sequences from NCBI
- Seek for multiple patterns using the FASTA IUPAC code for nucleotides
- Generate shuffled versions with a k-let parameter (Ushuffle algorithm)
- Results in a CSV format table
- Two modes of folding, localized or global (entire sequence)
- Folding with RNAFold (minimum free energy structure)
Project Samples
Categories
Bio-InformaticsLicense
GNU Library or Lesser General Public License version 3.0 (LGPLv3)Follow LoopMatcher
nel_h2
MongoDB Atlas runs apps anywhere
MongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
Rate This Project
Login To Rate This Project
User Reviews
Be the first to post a review of LoopMatcher!