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The three types of quasi-cliques we detect are: high density, low enrichment ("clique") subgraphs where Q contains every vertex of the graph; high enrichment, low density ("enriched") subgraphs with a small query set (every 10th vertex of V (G)); and moderate enrichment and density ("dense") subgraphs with a medium-sized query set (every 6th vertex of V (G)).
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Typically, G1 is a smaller query network such as a specific pathway of interest, and G2 is a large species-specific PPI network.
This is a surprisingly high number, but it correlates well with a recent study that used a smaller query set and a somewhat different methodology, and which estimated the number of different Rabs in the LECA to be up to 23 [ 5].
Given a small network (query) and a large network (target), network querying is to find the subnetworks of target similar to query.
Experimental evaluation and results are presented in Section 3. Section 4 presents two applications: automatic alignment of audio and lyrics in polyphonic music and a small-scale query-by-singing application.
I just have one small query - 48 hours?
For small query sets, the O lnn) behavior of the dichotomic search is the key.
This small query sequence provided sufficient adjacent, unique sequence to allow for unambiguous mapping of Alu-containing DNA to a single locus in the human genome.
Furthermore, to handle small query alignments and smoothen the scoring functions, we add pseudocounts depending on the query's mononucleotide background frequencies.
In the NATALIEQ setting with small query networks, the upper bound equals the score of the alignment found, thereby proving its optimality.
We define built-in queries as a small set of queries that are the most popular ones.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com