Sentence examples for using the sequence alignment from inspiring English sources

Nucleotide sequences were aligned using the sequence alignment program Clustal X [ 58] and were checked manually.

For the phylogenetic analysis of each gene, the corresponding protein sequences from representative taxa of plants, animals, fungi and protists were retrieved from NCBI (http://www.ncbi.nlm.nih.gov/protein/) and JGI with keyword searches and aligned using the sequence alignment software MUSCLE [ 114].

The mtDNA sequences were edited using the sequence alignment editor BioEdit 7.0.5.3 (Hall 1999) and aligned using the program Clustal X (Larkin et al. 2007).

Third, the deduced proteins for each of these paleolog sets were aligned using either Clustal and/or using the sequence alignment server at MAFFT (v. 6, http://align.bmr.kyushu-u.ac.jp/mafft/online/server/). The corresponding DNA alignment was manually inspected and adjusted.

Reads were aligned to the UCSC reference human genome assembly (hg19) using the sequence alignment software BWA version 0.5.10 [ 71] using the default parameters.

The final alignments were manually inspected and edited using the sequence alignment editor SE-Al version 1.d1 software [43].

Therefore, we mapped these amino acids onto a three-dimensional structure of hANT4, using the sequence alignments and the crystal structure of bovine ANT1 [16] as a guide (Fig. 4 and 8).

Phylogenetic analyses were conducted using the sequence alignments of these isolates and the references.

To analyze the evolution of the SlbZIP genes, an unrooted phylogenetic tree was generated using the sequence alignments of the SlbZIP proteins.

To analyze the evolutionary relationships of the PvTIFY genes, a phylogenetic tree was generated using the sequence alignments of TIFY proteins from common bean, soybean and Arabidopsis.

MODELLER used the sequence alignment from the Meta Server and the template PDB structure (1Q7F for Q03601 and 1D4X for Q20329) to generate five different homology models.