loopmatcher to run in windows online over linux online

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

Quick description about loopmatcher to run in windows online over linux online:

Multi-threaded application that searches for hairpin structures in cDNA / mRNA sequences (FASTA or GenBank) with specific consensus sequences in the loop. It implements RNAfold to predict the structure of the sequence, and UShuffle to generate random sequences with conservation of the k-nucleotide frequency. Also, it can download sequences in GenBank format directly from NCBI using the NCBI accession 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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