Abstract: A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.

Abstract: Ribonucleic acid interference molecules are provided. In one aspect of the invention, a method for regulating gene expression comprises the following step. At least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948, each one of the precursor sequences containing one or more mature sequences having SEQ ID NO: 103,949 through SEQ ID NO: 230,447, is used to regulate the expression of one or more genes.

Abstract: Ribonucleic acid interference molecules are provided. In one aspect of the invention, a method for regulating gene expression comprises the following step. At least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948, each one of the precursor sequences containing one or more mature sequences having SEQ ID NO: 103,949 through SEQ ID NO: 230,447, is used to regulate the expression of one or more genes.

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: 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 method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.

Abstract: Ribonucleic acid interference molecules are provided. For example, in one aspect of the invention, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948 and one or more mature sequences having SEQ ID NO: 1 through SEQ ID NO: 126,499 is provided. One or more of the at least one of one or more precursor sequences and one or more mature sequences may be computationally predicted, e.g., from publicly available genomes, using a pattern discovery method. In another aspect of the invention, a method for regulating gene expression comprises the following step. At least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948, each one of the precursor sequences containing one or more mature sequences having SEQ ID NO: 1 through SEQ ID NO: 126,499, is used to regulate the expression of one or more genes, e.g.