Sentence examples for using the multiple alignment from inspiring English sources
For phylogenetic analyses of each of these 10 species data sets, the sequences from each of them were assembled and aligned using the multiple alignment program CLUSTALW version 1.82 [1.82.
All proteins were aligned using the multiple alignment program CLUSTALX with default settings [ 18].
The mitochondrial sequences were aligned using the multiple alignment program of BioEdit [ 65] and manually checked and edited.
Deduced amino acid sequences were aligned using the multiple alignment ClustalW2 program (http://www.ebi.ac.uk/Tools/msa/clustalw2).ac.uk/Tools/msa/clustalw2
For phylogenetic analyses, rrs sequences of each of these 15 species were assembled and aligned using the multiple alignment program - ClustalX version 2.0.12 [ 73].
Nucleotide sequences of the 16S rRNA gene as well as nucleotide and amino acid sequences of the HSP were downloaded from GenBank databases (except for the Bx-62986 isolate) and aligned using the multiple alignment options in CLUSTAL followed by minor manual adjustments.
Using the multiple alignments of the FBG domains as queries, the secondary structure was predicted with the PHD program [ 27], which showed that the FBG domains have a highly conserved structure profile (Fig. 3).
For that purpose, specific primers of EV13 were designed by using the multiple alignments constructed with the available EV13 sequences employing Clustal X software (free software available from: URL: http://www-igbmc.u-strasbg.fr/BioInfo/).fr/BioInfo/
In their article, the authors used the multiple alignment method to reconstruct the evolutionary tree.
We used the multiple alignment of the CYTH domain to construct phylogenetic trees using the least squares, neighbor joining and maximum likelihood methods (see Materials and Methods).
Besides these analysis tools available for user selection, PRO-MINE uses the multiple alignment software for protein and nucleotide sequences – MUSCLE (Edgar, 2004) – in the internal pipeline.
