Sentence examples for method with alignment from inspiring English sources

Aself-optimized prediction method with alignment or SOPMA is employed for calculation of the secondary structural features of triose phosphate isomerase.

Thus, the signature method leads to a similar topology as the NJ method with alignment.

ExPASy's secondary structure prediction server (http://web.expasy.org/prot-param/) and selfoptimized prediction method with alignment (SOPMA) 23 were used to get an idea about the secondary structure of the chosen protein.

The phylogenetic analysis was performed using Neighbor-joining method with clustalx alignment of protein sequences with 1 000 repetition bootstraps.

In our case, the list is the output of each method, and with alignments of length 300 the list can extend up to 300 × 299/2 = 44850 pairs of sites.

The study established NATALIE as a top network alignment method with respect to both alignment quality and running time.

For the methods with face alignment, the EGM-rgbGE performed better except for the method by Wouter and Peter [19]; of course with face alignment, the EGM-rgbGE will perform better.

Because the lack of any methods to deal with alignment gaps properly in both programs, a cutoff of the percentages of sequence have data in PSP is used to filter the alignments column by column.

Genetic distance and average evolutionary divergence (D) were estimated using the Jukes-Cantor method [ 34]; positions with alignment gaps or missing data were eliminated in pairwise sequence comparisons.

Using the classical method for SNVs determination with alignment by BWA and variants detection and filtering (hard filter) by GATK, we identified 185,985 SNVs in the two runs from sample 509, and 190,426 SNVs in the two runs from sample 527 (Fig.  1a).

An improved version of the tree alignment method with extension to global and local forest alignments is given in Höchsmann et al. (2003) and implemented in the program RNAforester.