loopmatcher

We have hosted the application loopmatcher in order to run this application in our online workstations with Wine or directly.

Quick description about loopmatcher:

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)

Audience: Science/Research, Education.
User interface: Java Swing.
Programming Language: Java.
Database Environment: Flat-file.

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