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RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and(More)
The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3'(More)
We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. The proposed method is based on "secondary structure profiles". An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single(More)
Three-dimensional (3-D) structural models of RNA are essential for understanding of the cellular roles played by RNA. Such models have been obtained by a technique based on a constraint satisfaction algorithm that allows for the facile incorporation of secondary and other structural information. The program generates 3-D structures of RNA with atomic-level(More)
A convenient pattern-matching program using primary and higher-order structural features has been developed based on a 'backtracking' algorithm. A second implementation of the algorithm uses descriptors of structural features (including primary sequences) to align a list of homologous or highly similar sequences. An application of the pattern matcher to the(More)
BACKGROUND Differential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, each with its specific strength. Here, we analyze the vicinity of human polyadenylation signals in search of patterns that would help(More)
Selenocysteine is incorporated into selenoproteins by an in-frame UGA codon whose readthrough requires the selenocysteine insertion sequence (SECIS), a conserved hairpin in the 3'-untranslated region of eukaryotic selenoprotein mRNAs. To identify new selenoproteins, we developed a strategy that obviates the need for prior amino acid sequence information. A(More)
Natural killer cell and T cell subsets express at their cell surface a repertoire of receptors for MHC class I molecules, the natural killer cell receptors (NKRs). NKRs are characterized by the existence of inhibitory and activating isoforms, which are encoded by highly homologous but separate genes present in the same locus. Inhibitory isoforms express an(More)
The flexibility about seven torsion angles in nucleotides constitutes a severe obstacle to computer modeling of RNA. The computational feasibility of RNA conformational searches can be enhanced by assigning to each nucleotide a set of discrete conformations. In this work, four types of discrete conformational sets for the atomic representation of nucleotide(More)
BACKGROUND The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. RESULTS We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the(More)