DIALIGN | Multiple nucleotide sequence alignment

[…] elements was indicated by a 1 or 0 for each accession analysed and was collected into a data matrix. accessions belonging to the same lmw glutenin gene type were aligned and compared using the tools dialign [33] and clc genomic workbench (clc bio). consensus promoter sequences were generated using the algorithm of clc genomic workbench and were used to characterise the promoter types. conserved […]

[…] sequences from different sources for the same organism were combined. the coding regions on the genomic contigs are detailed in figure s3., multiple sequence alignments were generated using the dialign2 program [22]. zipk alignments were corrected to allow the arginine triplet at position 278–280 of the rodent sequences to align with similar triplets in the other sequences; this change […]

[…] searches were done as described in rueckert et al.[58] with nucleotide and amino acid sequences using the blastn- and blastp-algorithms [59]. multiple sequence alignments were performed using the dialign2 software [60]. the phylogenetic trees were calculated using the neighbor-joining method [61], which is integrated in the clustalx software package [62]. the results were visualized […]

[…] and products at 473 nm and filtered at 520 nm (fujifilm fla-3000). note that only one cleavage product was visualized, as only one strand was fluorescein labelled., sequences were aligned with dialign (27). phylogenetic analyses were performed with mega ver. 3.1 (28), using the maximum parsimony tool, and running the default setting of 1000 bootstraps. recombination analyses were performed […]