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Sequences were translated prior to alignment to preserve codon structure and then returned to nucleotide form for analysis.
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(You must have an authentic instructor to correct alignment and to preserve and strengthen the knees and back).
We obtained orthologous intronic D. simulans sequences from Hu et al. (2013), which was based on an updated D. simulans genome assembly and careful alignment procedures to preserve gene structures (http://genomics.princeton.edu/AndolfattoLab/w501_genome_files/alnMSY.tar.gz).edu/AndolfattoLab/w501_genome_files/alnMSY.tar.gz
DNA sequences of yaaW genes were aligned following [Pfam:UPF0174] protein sequence alignment, in order to preserve codon positions in the multiple DNA sequence alignment.
We believe that the characteristic of a correct global network alignment would be to preserve the relative functions of various network parts; this can be well-measured by the various GO enrichment analyses described above.
In cases of changes in the start or end positions between S. paradoxus and S. cerevisiae, the alignment was adjusted to preserve the start/end codons in S. paradoxus (so that no premature stop codons exist in S. paradoxus).
Sequence traces were edited using Sequencher (Gene Codes) software and multiple sequence alignments were generated using MUSCLE http://www.drive5.com/muscle/ with protein-alignment-assisted adjustments to preserve reading frames.
The sequences used for comparison were obtained from the GenBank database, aligned, and then corrected manually to preserve codon alignment and conserved motifs.
Further complications arise from the need to preserve alignment gap statistics.
The pkinase alignment was manually adjusted to preserve the conserved subdomains defined by Hanks and colleagues [ 118- 120] for eukaryotic kinases using the Se-Al Sequence Alignment Editor [ 137].
Sequences were trimmed to remove overhangs and aligned using ClustalW [54] without gap penalties to preserve structural alignments.
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