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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
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