Software and Projects in CBB Research Group

Softwares Descriptions
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 identity by descent (IBD) detection in large cohorts using positional Burrows-Wheeler transform

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