Sentence examples for multiple alignment used from inspiring English sources

Sequences assigned to each COG were aligned with ClustalW [ 17] using default parameters, and the resulting multiple alignment used to generate a distance matrix with the program PROTDIST, using default parameters (Jones-Taylor-Thornton model, where the distance is scaled in units of the expected fraction of amino acids changed), from the Phylip package [ 18].

A possible downfall of this method may arise when the majority of sequences in the multiple alignment used to generate a HMM are taken from closely related organisms.

Naturally, the choice of the weighting scheme for the multiple alignment used to obtain the consensus sequence or profile as well as the associated pseudocounts will also exert a significant influence on the result.

Genomic Evolutionary Rate Profiling (GERP; Cooper et al., 2005) score was used to calculate the conservation of each nucleotide in multi-species alignment The multiple alignment used to derive GERP score is the 29-way EPO alignment.

The multiple alignment used to drive the phylogenetic analysis summarized in Figure 3 was constructed as follows: 1) A representative set of FADS-type I and FADS-type II sequences were multiply aligned with CLUSTALW [ 38] and their secondary structure was predicted with PSIPRED [ 40] taking the Thermotoga maritima sequence as a representative.

In addition, the multiple alignment used for the phylogenetic analysis revealed two highly conserved regions (about 90% PSI between human, mouse and dog), i.e. the N- and C-terminus ends (amino acids 1 98 and amino acids 420 647, respectively), and a more divergent central region (≤50% PSI).

These clusters were aligned by Multiple Alignment using Fast Fourier Transform MAFFTT) (Katoh et al. 2002) and concatenated, followed by tree construction using PhyML (Guindon et al. 2010).

Protein sequences of BVMOs (Additional file 1: Table S1) were aligned with MAFFT (Multiple Alignment using Fast Fourier Transform) version 7 (Katoh and Standley 2013).

Sequences were aligned with MAFFT (multiple alignment using fast Fourier transformation, v6.832b) using the "G-INS-I" parameters [ 28].

The new sequences (31) were re-aligned to the original multiple alignment using T-coffee.

Sequences were aligned using the MAFFT (Multiple Alignment using Fast Fourier Transform) web server at the European Bioinformatics Institute [ 57].