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RScan employs RNAfold to predict the secondary structures of queries and segmented sequences.
Because each query produced only one high-scoring hit located between HoxC11 and HoxC12, the structures of queries determined by PMmulti and Infernal should be reasonable.
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Structures of query proteins can be predicted if suitable templates can be detected.
By formulating the network querying problem as a conditional random fields (CRF) model, which is widely used in the fields of machine learning, we designed efficient algorithms specific to different structures of query networks.
However, recent work has shown that this feature could play a very useful role in query answering, where the syntactic structure of queries means that the occurrence of state variables is restricted in a way that allows for decidable reasoning.
In other words, the neighbor structure of query vertex v should be preserved around vertex u in RDF graph.
In this paper, we propose a novel matching technique based on the positions of attributes appearing in the schema structure of query results.
RScan can use the parameters with very strict thresholds to quickly search similar structures of the query in Rfam seed structural database (see Methods).
This tab contains a table, which displays the 2D structures of the query and reference fragment pairs and their corresponding HDs.
Moreover, Infernal uses consensus sequences and structures of the query sRNAs instead of single sequences.
3D-BLAST searches the SADB using this SASM to quickly discover homologous structures of a query protein.
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