Bioinformatics 101: RNA Sequence Analysis

miRNA Resources:

• MirBase
• free database of miRNA sequences
• TarBase
• free database of experimentally validated miRNA targets
• miRecords
• database of miRNA-target interactions
• IPA miRNA-target analysis
• commercial database that includes free databases as well as a proprietary list of miRNA-target interactions found using text-mining of the literature
• TargetScan
• free tool to predict miRNA targets
• sylArray
• tool to predict miRNA targets from gene expression data.  Uses gene ranking, so it doesn't require mRNA differential expression (although you will need to check that the miRNA regulator is differentially expressed)

In general, I think you really need both miRNA expression and mRNA expression data to get reliable results when trying to identify miRNA-target interactions

RNA-Seq Splicing Events:

• JunctionSeq - extends DEXSeq to include junction coverage (including junctions not defined among isoforms in reference database).  Strictly speaking, it only calls differential exon and junction coverage (and provides a statistic at the gene-level), but the junction coverage can be helpful in identifying some other types of splicing events.
• MATS - Provides differential splicing for skipped exon (SE), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), and retained intron (IR)
• MISO - Provides single-sample and differential splicing for skipped exon (SE), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), retained intron (IR), tandem 3' UTRs (TandemUTR), alternative first exon (AFE), and alternative last exon (ALE)

RNA Secondary Structure:

• Mfold
• RNAfold

RNA Domain Homology:

• Rfam
• may be helpful in predicting function of a non-coding RNA of unknown function

de novo Assembly Algorithms (RNA-Seq):

• Oases
• Trans-ABySS
• Trinity
• eXpress - mRNA quantification tool that works with both de novo assembly transcripts (as well as transcripts from direct genome alignment)

RNA-Seq QC

• FASTX-Toolkit - popular suite of tools to quantify and manipulate sequences .fastq and .fasta files
• samtools - popular suite of tools to quantify and reformat .sam/.bam files
• Picard - Java-based implementation of samtools; CollectRNASeqMetrics can produce a coverage plot (normalized per start to end of transcript)
• RSeQC - package to produce a variety of RNA-Seq QC figures

General RNA-Seq Analysis

• Wikipedia list of RNA-Seq bioinformatics tools
• Please see Gene Expression Analysis for tools for statistical analysis of RNA-Seq data