| 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 |