Sentence examples for for our alignment from inspiring English sources

For our alignment, protein-coding genes were constrained to align by codon and tRNA-coding genes were constrained to align by regions of potential secondary structure [ 38].

Herein, the two subsets for our alignment in AVANA were i) 8 MMP-13 sequences and ii) all other MMPs (42 of them).

Table 2 shows the pseudocode for our alignment clustering method.

It is therefore also promising to develop improved objective function for our alignment approach.

In this section, we present a new translation-dependent scoring system suitable for our alignment algorithm.

We could significantly reject the possibility of sequence saturation for our alignment (Additional File 4).

Per-site substitution rates were calculated for our alignments using HyPhy (Pond et al. 2005), and the fastest evolving sites were removed using SiteStripper v.1.01 (http://www.phycoweb.net/software/SiteStripper/index.html, last accessed October 9, 2014), leaving a percentage length of the original alignment (95%, 80%, and 70%).

Figure 5 Location of the centers of mass of single cross-sections for each projection angle (blue) and the least squares solutions to fit the viable paths (red) given by Equation 3. The results from cross-correlation for two cross-sections are given in (a, c), and the results from our alignment method for the same cross-sections are shown in (b, d).

The latter result has important consequences for the further development of our alignment approach: it seems worthwile to develop more efficient algorithms for the optimisation problem that arises in the context of the DIALIGN algorithm.

An amino acid residue consensus was also determined for each SMR subclass from our alignment and the results are presented as percent occurrence in Figure 5. SMR proteins alignments to BAT, DMT and MFS transporters were performed using ClustalW and manual alignment using the editing program GeneDoc (v 2.5.010 [ 64]).

Based on these results, we conclude that SCOW is a state-of-the-art alignment method for gene-expression time series, and we therefore use it as the core alignment method for our clustered alignment approach.