Many small, non-coding RNAs (sRNAs) act as post-transcriptional regulators of messenger RNAs by base-pair binding to these targets. is a program which, given the sequence of a small RNA gene, searches the entire genome of a species for potential targets of the sRNA gene's action.

sRNA Options

Species	The genome in which searches for targets of the given sRNA gene.
sRNA	provides a list of known sRNA genes (the list, of course, is incomplete). The user has the option of searching for targets of one of these known sRNA genes or else searching for targets of an sRNA gene whose sequence is input by the user.
sRNA Sequence	The user inputs the nucleotide sequence of an sRNA gene. will search for targets of this sRNA gene's action.
Remove terminator	will automatically identify and remove the terminator stem-loop of the sRNA sequence. Often, the terminator stem-loop does not participate in the sRNA:mRNA interaction.

Target Options

Focus around start codon	Many sRNAs interact with their target genes around the targets' translation start sites and ribosome binding sites. The user can restrict the search for target interaction to the neighborhood around a message's start codon. If the user enters the sentinel neighborhood (0,0) then the program will search the entire coding sequence of a gene for a target interaction.
Hybridization seed	will only report target interactions which contain at least a certain number of consecutive base-pairings as specified by the hybridization seed. To obtain all target interactions, the user should set the hybridization seed to 0.
G:U pairs in seed	Allow G:U basepairs when determining the consecutive base-pairings in a hybridization seed.
Single target	Rather than search an entire genome for target interactions with the given sRNA, will only search for an interaction with one particular gene as specified by the gene's name.

Scoring Options

P-value threshold	Only report target interactions with a P-value below this threshold.
Thermodynamic energy scoring	will identify and score targets based on the minimum free energy of the target interaction with the sRNA gene. The energy of the hybridization is calculated using the thermodynamic parameters employed by MFOLD version 3.0 (Zuker, Nucleic Acids Research, 31 (13), 3406-15, 2003).
Orthologous genes	For a given sRNA gene, will first attempt to identify orthologous sRNA genes in related species (generally, orthologous sRNAs are found only in closely related species). If an orthologous sRNA gene is found in another species' genome, then will determine the hybridization of the ortholgous sRNA to orthologous mRNA targets.