Softwares and Projects from UCF-CBB Research Group

PAL

Pseudoknotted RNA ALignment

RNAscf

Consensus folding of unaligned RNA sequences

PMFastR

A New Approach to Multiple RNA Structure Alignment

RNAMotifScan

Automatic identification of RNA structural motifs

TreeLign

Automatic update of 16s rRNA Phylogenetic Tree and Multiple Sequence Alignment in Metagenomics (updated: Dec 1 2009)

FitchAln

Given phylogenetic tree and multiple sequence alignment, show the Fitch score matrix.

miRNA Target Prediction

microRNA Target Prediction using TargetScan (updated: Sep 13 2009)

RNAEAPath

Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks

RNASLOpt

Predicting stable local optimal structures for RNAs (e.g. riboswitches)

RNAConSLOpt

Predicting consensus stable local optimal structures for aligned RNA sequences (e.g. riboswitches)

Pseudo RP Gene Expression

Expression profile of ribosomal protein pseudogenes in 16 human tissues

Fly3UTRCluster

Discovering Non-coding RNA Elements in Fly's 3'UTRs by Structural Clustering

PhyloRNAalifold

Predicting consensus structures in RNA alignments by incorporating RNAalifold with phylogenetic information

ProbeAlign

Annotating ncRNA secondary structures with high-throughput sequencing based structure probing information

ERA

Efficient alignment of RNA secondary structures using sparse dynamic programming

MutualFold

Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing based RNA structure probing

STAR3D

A program for RNA 3D structure alignment

WebSTAR3D

A web server for RNA 3D structure alignment

CompAnnotate

A program for annotation of RNA using comparative method

RaPID

Ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts

RNAMotifContrast

Visualization of RNA Structural Motif Variations and Discovery of Subfamilies

RNA-NRD

A Non-redundant RNA Structural Dataset for Benchmarking and Functional Analysis

RNAMotifComp

A comprehensive method to analyze and identify structurally similar RNA motif families

RaPID-Query

RaPID-Query for fast identity by descent search and genealogical analysis

CircularSTAR3D

A stack-based RNA 3D structural alignment tool for circular matching

Recomb-Mix

Fast and accurate local ancestry inference with Recomb-Mix