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For each family, we will use the multiple alignment of contact maps corresponding to each PPI complex within the family and generate aligned core regions within each sequence pair.
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In our experiments, we use the multiple alignments and phylogenetic tree given in Kellis et al. (2003).
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.
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
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.
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].
Full-envelope protein sequences for each serotype were aligned by using the multiple alignment tool of MEGA5 (www.megasoftware.net).net
The PCR products were sequenced and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program.
All sequences were aligned and homology was calculated by using the multiple alignment algorithm in the MegAlign package (Windows version 7.1.0; DNASTAR, Madison, Wis).
Mature and precursor sequences of miRNAs across animal species were aligned with Clustal X 2.0 [35] respectively by using the multiple alignment.
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