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The sequences of LuxS orthologs were aligned and a phylogenetic tree was built from the alignment.
Using the model built from the alignment of 33 seed-sequences, the search resulted in 395 potential U5 sequences, including the previously reported U5 candidate [8].
Then, for each core block, a weighted profile is built from the alignment and each sequence within the subfamily is assigned a score against the profile.
For each block in each subfamily, a profile [62] is built from the alignment and pairwise profile-profile comparisons are made to identify blocks shared between a number of subfamilies.
Next, a maximum likelihood tree is built from the alignment by PHYML (substitution model: HKY; Transition/transversion ratio∶4.0; Proportion of invariable sites: program estimated; Number of substitution rate categories: 1; Gamma distribution parameter∶1.0; Starting tree: BIONJ distance-based tree; No starting tree optimization) [41].
A covariance model was built from the alignment and searched against fully sequenced bilaterian genomes using INFERNAL 1.0 (Nawrocki et al, 2009).
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At this point, models can be built from the alignments and the structural information of each template.
Protein sequences for each group were aligned with MUSCLE v.3.5.1 [ 71], and Hidden Markov Models (HMMs) [ 72] were built from the alignments using hmmbuild v.3.0 [ 73].
Phylogenetic trees were built from the alignments by the bootstrap test of phylogeny (3,000 replications) using the neighbor-joining method with a Poisson correction model.
To achieve this efficiently, we build from the alignment maps a variant of the de Bruijn graph, here called the PE multi positional de Bruijn graph.
Each Pfam-A family consists of a curated 'seed alignment' containing a small set of representative members of the family, profile hidden Markov models (profile HMMs) built from the seed alignment, and an automatically generated full alignment, which contains all detectable protein sequences belonging to the family, as defined by profile HMM searches of primary sequence databases.
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built from the grass
built from the back
built from the genome
built from the rubble
built from the accident
built from the universe
built from the bottom
built from the waterfront
built from the perspective
built from the login
built from the year
built from the InputStream
built from the top
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built from the inside
built from the transmitter
built from the design
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