Tool
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Description
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Link
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MMSEQ
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Haplotype- and isoform-specific expression estimation using multi-mapping RNA-seq reads
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Cufflinks/Cuffdiff/Cuffcompare
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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
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RNAsnp
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Predicting SNP effects on local RNA secondary structure
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RIsearch
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RIsearch is a program for fast RNA–RNA interaction search
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RNAz
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RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures
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RNAclust
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RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs
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ORF Finder
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The ORF Finder is a tool which finds all open reading frames of a selectable minimum size in a user’s sequence
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Pfam
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The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models
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Rfam
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The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures, and covariance models
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- 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]