The flowchart illustrates the basic functionality of the EST2ncRNA pipeline. Furthermore, the number of PigEST conread candidates are shown for each step. The pipeline detects known and novel candidates of functional non-coding RNAs as well as cis-regulatory elements from large assembled EST datasets. In summary, the pipeline consists of four main steps: (1) pre-annotation of known ncRNAs, (2) homology search in other organisms, (3) prediction of thermodynamic stable and conserved RNA structures, and (4) post-annotation. A method to detect family specific RNAs in the post-annotation is RNAmicro for instance. The candidates for mRNA hybridization predicted by RNAduplex are not included in the publication. The sign × indicate sequences not matching a given step in the pipeline. The sign √ indicate the sequences which were matched. (*) 18 ORF-free conreads contain two independent RNA structures of which only one is similar to an human UTR. Therefore, these conreads are counted twice.