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Table 1lists bona fide Drosophila miRNAs that scored in the top 208, grouped as members of the reference set followed by newly identified miRNAs that fulfill accepted criteria for miRNA biogenesis (that is, ones whose expression was confirmed here by northern blot and/or are homologous to miRNAs cloned in other species); each subset is rank-ordered by miRseeker score.
Computational prediction of DrosophilamiRNA genes using miRseeker
The first 208 candidates produced by miRseeker, along with information on structures, scores, alignments, and genomic locations, are accessible via the web [ 43 ] .
To allow public access to miRseeker, we developed a scaled-down version of our computational pipeline [ 58 ] . It allows a user to input two sets of homologous sequences (up to 100 kb) from any two species along with gene annotation for one of them, and performs all the steps of the miRNA-finding procedure described above, producing a list of miRNA candidates ordered by score.
miRseeker subjects conserved intronic and intergenic sequences to an RNA folding and evaluation procedure to identify evolutionarily constrained hairpin structures with features characteristic of known miRNAs.