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RNA Structure Prediction

RNAstructure – Suite of programs from the David Mathews group that make use of the Turner free energy parameters to predict RNA secondary structure, calculate base pair partition functions, predict pseudoknots, and more!

The Vienna Package – Another suite of programs to analyze RNA structure, also has a convenient web server.

RMDB structure server – Predict RNA folding on-line by incorporating pseudo-energy constraints from biochemical mapping data.

RNA Pseudoknot Prediction

DotKnot – Algorithm that makes use of base pair probabilities to build potential pseudoknots.

pknotsRG – Heuristic algorithm for predicting a restricted class of pseudoknots.

Knotseeker – Find pseudoknots in relatively large RNA fragments.

Structured RNA Discovery

RNAz – Find regions with potentially conserved RNA structure. Also has convenient webserver.

RNA Alignment Programs and Editors

MAFFT – An excellent alignment tool that has RNA-specific options that really set it apart from other alignment programs. Webserver also available.

BioEdit – Great free alignment editor that also contains Clustal alignment program.

Geneious – A very nice commercial alignment editor program with a useful free version and even better functionalities available (for a price). Also has a nice cladistic tree editor that allows for sub alignments to be extracted easily.

RNA Alignment Programs and Editors

lincipedia – A comprehensive compendium of long non-coding RNAs

miRcode – Transcriptome-wide microRNA target prediction including lncRNAs.

miRBase –  Database of known and putative microRNAs.

Dfam – DNA families database of repetitive elements.

UTRdb – Database Pagesof UTRs.

lncRNA db – Long non-coding RNA database.

NPinter – database of ncRNA interactions (e.g. miRNA targets).

Useful Tools

Tandem Repeats Finder  – Find tandem repeats in a sequence.

FeaturesExtract – Get features (e.g. CDS) from GenBank files.

Elsevier Methods Navigator – Protocol: Computational Prediction of RNA Secondary Structure.

NIH File Format Conversion – Handy tool to convert between sequence files.

File Format Conversion – web server that allows one to switch between different file formats: e.g. fasta to clustal alignment formats.

OligoCalc – Web tool to calculate nucleic acid molecular weight, melting temp., extinction coefficient, etc.

DAVID Bioinformatics Database – Gene ontotolgy (GO) term analysis tools.

Branch Point SVM – predict mammalian branch point sites.

RNApdbee – database to convert PDB 3D structures (including pseudoknots) into 2D images.

Protein 3D Alignment

SuperPose – Easy Webserver to align protein 3D structures.

CID-miRNA – Prediction of pre-miRNAs.

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