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The program TargetMiRna is developed for search for microRNA (miRNA) sites in genomic sequences. miRNAs promote mRNA cleavage at almost perfect complementarity to its site. In case of less complementarity, miRNAs inhibit mRNA translation. Our program TargetMiRna searches a given target sequence for microRNA sites, basing on calculation of the interaction energy between miRNA and its site. Therefore TargetMiRna can be used for search of both site types.

TargetMiRna scans a target sequence and calculates the energy of complementary interaction between miRNA and possible site i as follows:

where eh is helix energy and el is loop energy if any.

The energy parameters of complementary interactions and loops are taken from Turner's table. To skip suboptimal miRNA-site pairing we minimize the interaction energy by a dynamic algorithm which is based on Nussinov and Jackobson and Zuker papers. The user sets an energy threshold, and TargetMiRna outputs all the candidate sites, which energy of miRNA-site interaction is lower (i.e., more stable) than it.

TargetMiRna supports two different search modes. In the first mode the user inputs a single miRNA sequence by himself. In the second mode the user specifies the organism and our program searches for the sites for all miRNAs known for this organism, using built-in miRNA library. Currently the library contains the miRNAs of the following organisms:
cel (Caenorhabditis elegans)
hsa (Homo sapiens)
dme (Drosophila melanogaster)
mmu (Mus musculus)
ath (Arabidopsis thaliana)
rno (Rattus norvegicus)
oza (Oryza sativa)
ebv (Epstein Barr)
gga (Gallus gallus)
dps (Drosophila pseudoobscura)
dre (Danio rerio)
xla (Xenopus laevis)
zma (Zea mays)
sbi (Sorghum bicolor)
ame (Apis mellifera)
aga (Anopheles gambiae)
cfa (Canis familiaris)