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)

Project Samples

Capture from FORNA web app using link auto-generated

Project Activity

See All Activity >

License

GNU Library or Lesser General Public License version 3.0 (LGPLv3)

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LoopMatcher Web Site

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Additional Project Details

Operating Systems

Windows

Intended Audience

Education, Science/Research

User Interface

Java Swing

Programming Language

Java

Database Environment

Flat-file

Related Categories

Java Bio-Informatics Software

Registered

2019-11-22

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