Sentence examples for embedded alignment from inspiring English sources

Sequences for each locus were aligned in Geneious V6 (BioMatters) using the embedded alignment tool, and manually inspected, and corrected.

The ML tree based on the JTT + Γ4 amino acid substitution model was calculated using the MEGA5 program (Tamura et al. 2011) and the embedded alignment software MUSCLE (Edgar 2004), with a data set including all obtained sequences plus homologs identified by Ensembl.

Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences.

Despite the great potential of the embedded alignment strategies in answering a diverse set of biological questions, their computational costs are prohibitively expensive, a problem that arises out of the current method of generating and analyzing embedded sequences.

We performed analyses on a structurally resolved (X-ray Crystallography) transmembrane protein called Bovine Rhodopsin (PDB: 1F88) in order to determine the information contained in a pure population of embedded alignments [27].

Culture is not merely a feel-good concept, rather it is the driver in the organization that, if truly embedded, creates alignment within the team.

Similar to phylogenetic profiles, our embedded-alignment profiles present a protein as a vector where each entry quantifies the existence of alignments with a PSSM [1], [2].

Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains.

We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter) provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships.

Unfortunately, most methods require at least two structures to be embedded in the alignment, a condition rarely met when dealing with standard datasets.

In order to identify potential functional motifs of MazF proteins, phylogentic analyses of MazF proteins were conducted by applying the embedded multiple sequence alignment ClustalW program in the Geneious software package v 5.5.7 [ 76, 77] with the Neighbor Joining method.