MaxAlike

Webserver and Software

Phylogenetic reconstruction of in­com­plete sequences by maximum like­li­hood.

PETfold and PETcofold

Webserver

Phylogenetic, Evolu­tionary and Ther­mo­dy­na­mic fol­ding of a multiple alignment of RNA se­quen­ces.

• PETfold: Phylogenetic, Evolu­tionary and Ther­mo­dy­na­mic folding of a multiple alignment of RNA se­quen­ces.
• PETcofold: Integrated frame­work with PETfold to fold and search for RNA-RNA interac­tions between two multiple alignments of RNA se­quen­ces.

deepBlockAlign

Software

A tool for aligning RNA-seq profiles of read block patterns.

Clasp

Software

Fast local fragment chaining using sum-of-pair gap costs.

Non-coding RNA tracks

Data Resource

Collection of ncRNA predictions in UCSC style.

WAR

Webserver

Webserver for aligning structural RNAs.

FOLDALIGN

Webserver and Software

Pairwise local and global structural alignment of RNA sequences.

• FOLDALIGN: Pairwise local and global structural alignment of RNA sequences.
• FOLDALIGNM: Multiple glo­bal struc­tu­ral a­lign­ment of RNA se­quences

The R_K Page

Webserver and Software

Computing the K category correlation coefficient.

RNAdbtool

Webserver and Software

Semi-automated update and cleanup of structural RNA databases.

MatrixPlot

Webserver and Software

Visualize sequence and structure constraints.

RNA Structure Logos

Webserver

Visualize the information content of DNA and RNA sequence and structure alignment.

Protein Logos

Webserver

Visualize the information content of protein sequence alignments.

distanceP

Webserver

Prediction of distance constraints in proteins.

KVL Assembly demo

Webserver

Sequence assembly for toy pur­poses.

FOLDALIGNM

Software

Multiple glo­bal struc­tu­ral a­lign­ment of RNA se­quences

SARSE

Software

Semi-Automated RNA Sequence Editor.

Micro RNA structurally clustered

Data Resource

MicroRNAs clustered by their structure.

cmf_encode

Data Resource

CMfinder predicted conserved RNA structures in the ENCODE regions using RNA structure constraints.

PigEST

Data Resource

Porcine EST assembly, expression and SNP data.

• PigESTncRNA: Noncoding RNAs.
• PigESTmap: Genomic mappings.
• PigESTmito: Porcine mitochon­dria. Expression and SNPs.

HM ncRNA scan

Data Resource

Predicted conserved RNA structures in corresponding region between human and mouse unalignable in primary sequence.

Piggenome DK

Data Resource

Genomic sequences from the Sino-Danish pig genome project.

tmRDB

Database

tmRNP Database (local mirror). In­clu­des struc­tural a­lign­ment of tmRNA sequences.

SRPDB

Database

Signal recognition particle database (local mirror). In­clu­des struc­tural a­lign­ment of the SRP RNA sequences.

telomDB

Database

Telomerase Database (local mirror).