In response, various optimization models have been proposed to establish alignments that meet various geometry requirements.
We use these distance measures to construct phylogenetic trees for real-world and simulated DNA and protein sequence families, and we compare our method to established alignment-free methods using contiguous -word frequencies, as well as to a traditional alignment-based approach.
We therefore used three-dimensional structure-based alignments including available NMR models together with secondary structure prediction (Jones, 1999) and manual curation of the aligned sequences to establish an alignment of all human BRDs.
In keeping with the use of functional similarity to establish the alignment, PINALOG finds more functional alignments (NF).
To establish the alignment of the sort plate on the sort stage we performed sorts of 10 beads onto the lid of a 96-well plate.
By analyzing the course of the Risk Model project and its contributions, we wanted to establish which alignment efforts are important for the RIVM-Inspectorate context in order to find clues for improving the contributions of RIVM projects.
In this regard, the first step was to establish the alignment size and identity percentages of cut-offs, being 89.58 and 50.00%, respectively, for SEC putative proteins, whereas for PSE putative proteins, these cut-offs were 88.16 and 48.80%, respectively.
A total of 315 gene-based markers mapped to the Lp1 family were used for establishing alignments with Os, Bd and Sb.
The twist drill was used to establish the axial alignment of the implant and to assist in the guidance of the depth drill.
To confirm homology between the procaryotic piwi mid domain and the Ago family of sequences and to establish an initial alignment, a sequence corresponding to the mid domain of the A. aeolicus Argonaute structure ([PDB: 1yvu], range 349 484) was used as a PSI-BLAST query (E-value cutoff 0.005, maximum 20 rounds, NR database).
In most cases, phylogenetic trees calculated with kmacs were more accurate than trees produced with established alignment-free methods that are based on exact word matches.
