RNA sequence databases

Pairwise comparison of two sequences is a fundamental process in sequence analysis. It defines the concepts of sequence identity, similarity, and homology as applied to two proteins, DNA or RNA sequences. Database interrogation can take the form of text queries or sequence similarity searches. Typically, the user employs a query sequence to conduct sequence similarity search so that the relationships between the query sequence (probe) and another sequence (target) can be quantified and their similarity assessed. 

Ribonucleic acids play vital roles in the flow of genetic information. A large number of RNA sequence databases, as given in Table 15.7, illustrate different types of RNA and their functional diversities. 

Single nucleotide polymorphisam databases Various RNA sequence databases ... 

The final method of RNA structure prediction, empirical algorithms, are also analogous to primary-structure motif detection methods. Known RNA structural motifs are extracted from structural databases, and the primary-structure patterns underlying these motifs are identified. Novel RNA sequences are then scanned for these primary-structure motifs much like a novel protein sequence might be scanned for CDs. In essence, these methods search the primary structure of sequences for conserved motifs that indicate secondary structure. One of the most flexible and powerful empirical tools is RNAMotif, which is freely available for download, but does not have an associated web-server (23). 

Properties such as thermodynamic values, sequence asymmetry, and polymorphisms that contribute to RNA duplex stability are taken into account by these databases (Pei and Tuschl 2006). In addition, artificial neural networks have been utilized to train algorithms based on the analysis of randomly selected siRNAs (Huesken et al. 2005). These programs siphon significant trends from large sets of RNA sequences whose efficacies are known and validated. Certain base pair (bp) positions have a tendency to possess distinct nucleotides (Figure 9.2). In effective nucleotides, position 1 is preferentially an adenosine (A) or uracil (U), and many strands are enriched with these nucleotides along the first 6 to 7 bps of sequence (Pei and Tuschl 2006). The conserved RISC cleavage site at nucleotide position 10 favors an adenosine, which may be important, while other nucleotides are... 

Sequence databases generally specialize in one type of sequence data, i.e. DNA, RNA or protein (Higgins and Taylor, 2(XX)). Structure data must unambiguously define the atomic connectivities and the precise three-dimensional coordinates of all atoms within the molecule. These sequences and structures are the itans to be eomputed on and worked with as the valuable components of the primary databases. Generally, the gateways to sequence and structure databases include ... 

Nucleic acid sequence databases typically contain sequence data, which includes information at the level of the gene structures, introns and exons (for eukaryotics), cDNA (complementary DNA), RNA and transcription regulations. The important nucleic acid sequence data repositories as the primary resources known as International Nucleotide Sequence Database Collaboration (INSDC) are ... 

All primary sequence databases provide tools for essential sequence analyses. Many servers are also available on the web to perform useful computation on DNA/RNA sequences and structures. These web servers (Table 15.9) provide an array of diverse computational genomic tools. 

EMBL The EMBL is a molecular biology research institution supported by 20 European countries and Australia as an associate member state. It is Europe s pri-maiy nucleotide source. We can find out nucleotide sequences and much more data from it. It is the main source for DNA and RNA sequences. The database is a result of the collaboration between GenBank (USA) and the DDBJ. 

Wang X, Slebos RJ, Wang D, et al. Protein identification using customized protein sequence databases derived from RNA-Seq data. J Proteome Res. 2012 11 1009-17. doi 10.1021/pr200766z. 

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