Efficient target prediction incorporating accessibility of interaction sites

Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing

A tool for de novo clustering of long transcriptomic reads

Parallel solution for local RNA secondary structure analysis

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

RNAnue

RNA Interaction Format (RIF) with reference implementations in C++, JavaScript, and Python

C++ Tandem Repeats Detector -- Spring 2020 Independent Study Class in the Computer Science Department of Brooklyn College

LaRA 2: Lagrangian Relaxed structural Alignment

Translate nucleotides (DNA & RNA) to aminoacid using IUPAC ambiguity codes

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

bamcc — split SAM/BAM files into connected components

RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding

MFE method for predicting the psuedoknotted secondary structures of RNA sequences.

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding

A C++ software interface to RNA module databases, and a biobjective algorithm to include known modules in sequences to assist the energy criteria in predicting secondary structures.

Code for systematically classify data in SRA according to all the taxa present in the reads (SRA-metagenome)

Supplementary files

HiPR: High-throughput Probabilistic inference of RNA structure