Abstract: In one aspect of the invention, a method for regulating the expression of a transcript comprises using at least one interfering RNA molecule that binds to an area of transcript containing a region that corresponds to at least one sequence having SEQ ID NO: 1, the interfering RNA molecule regulating the expression of the transcript through post-transcriptional silencing. In another aspect, a method for regulating the expression of a transcript comprises at least one of the provided sequences having SEQ ID NO: 1 being used to design an interfering RNA molecule that contains a region that corresponds to the reverse complement of one or more sequences having SEQ ID NO: 1, the interfering molecule regulating, through post-transcriptional silencing, transcripts that contain the sequence having SEQ ID NO: 1.

Abstract: Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.

Abstract: A computer-implemented method and a computer system for identifying a phylogenetic tree from a plurality of biological sequences is provided. Each biological sequence is associated with a sampling date. First, the plurality of biological sequences is aligned and a distance matrix is obtained. Then, a subset of these sequences without any duplicated sequences is selected and a directed graph representation of the subset of biological sequences is generated based the associated sampling dates. Then, a minimum spanning tree is computed from the weighted directed graph representation. Then, in an iterative procedure, the sequences of unsampled evolutionary intermediates are inferred from mutation patterns that reflect the difference in sequence between the nodes in the minimum spanning tree. The new sequences are added with associated time stamps to the sequence set. Then, sets of identical sequences are removed. Then, an optimum branching is recomputed. This step is repeated until no new intermediates are found.

Abstract: Sequences that can be used in the context of controlled gene regulation are provided. In one aspect, at least one sequence comprising at least one of one or more sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326 is provided. One or more of the provided sequences may be computationally predicted, e.g., from publicly available genomes, using a method based on pattern discovery. In another aspect, a method for regulating the expression of a transcript comprises the step of said transcript containing a region that corresponds to at least one of the provided sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326, the region being targeted either by a naturally occurring, or appropriately designed, interfering RNA molecule that regulates the expression of said transcript through post-transcriptional silencing.

Abstract: Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.