Sentence examples for build from the alignment from inspiring English sources

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.

We used the species tree known for the Silene species in the alignment [ 56] instead of the tree built from the alignment because of tree building problems with less than 10 sequences (as in [ 34], see Additional file 5, figure S5).

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].

The unrooted phylogenetic tree was built from the alignment of the FL-amino acid sequences of 51 GmARFs and 23 AtARFs.

A tree built from the alignment revealed a highly divergent subfamily of 830 putative ABC transporters (based on the presence of ABC_tran, ABC_tran_2, and/or AAA_21 domains).

A covariance model was built from the alignment and searched against fully sequenced bilaterian genomes using INFERNAL 1.0 (Nawrocki et al, 2009).

A matrix X of size m × n can be built from the alignment, where m is the number of reads and n is the number of heterozygous sites.