Words similar to clustal
Example sentences for: clustal
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The amino acid sequences of the Runt domains of all each of the collected genes, together with two previously described sequences from the spider Cupiennius salei [ 15 ] , a sequence from the crayfish Pacifastacus leniusculus , and one from the nematode Meloidogyne hapla , were aligned using Clustal W [ 16 ] , as shown in Figure 2. Functionally, the Runt domain is required both for DNA binding and for interaction with its heterodimeric partner (the beta subunit), which serves to allosterically enhance the DNA binding of the Runt domain [ 1 14 ] . Superposition of the alignment and the known crystal structure of mouse Runx1 [ 14 17 ] reveals that residues that make either direct or indirect contact with DNA are invariant (marked by asterisks in Fig.
Examination of the Clustal X-alignment of all the protein sequences revealed significant structural differences (Figure 3).
Parameters for CLUSTAL alignments were: Pairwise alignment: Ktuple, 1; gap Penalty, 3; windows, 5; diagonals saved, 5. Multiple alignment: gap penalty, 10; gap length penalty, 10.
Sequences were aligned using CLUSTAL X 1.8 [ 45 ] . The number of substitutions per site in the aligned data set were calculated using a JAVA program written by Olga Zhaxybayeva (University of Connecticut).
Protein alignments were generated using the Clustal X program and checked manually [ 40 ] . SSU NA sequences were aligned using Clustal W as implemented by the OMIGA package and checked manually [ 41 42 ] . NA alignments of full-length moeZ sequences for indel analysis were aligned manually based on the Clustal X protein sequence alignment.
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