Nice list of Tools for RNA Research

Tool
Description
Link
MMSEQ
Haplotype- and isoform-specific expression estimation using multi-mapping RNA-seq reads
Cufflinks/Cuffdiff/Cuffcompare
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
RNAsnp
Predicting SNP effects on local RNA secondary structure
RIsearch
RIsearch is a program for fast RNA–RNA interaction search
RNAz
RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures
RNAclust
RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs
ORF Finder
The ORF Finder is a tool which finds all open reading frames of a selectable minimum size in a user’s sequence
Pfam
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models
Rfam
The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures, and covariance models
  • Papait R, Kunderfranco P, Stirparo GG, Latronico MV, Condorelli G. (2013) Long Noncoding RNA: a New Player of Heart Failure? J Cardiovasc Transl Res [Epub ahead of print]. [article]

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