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Example sentences for: aligned
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The Z-score provides a measure of the statistical significance that can be compared among pairs of aligned profiles.
Approximately 8500 16S and 16S-like rRNA sequences and 1050 23S and 23S-like rRNA sequences were collected from all branches of the phylogenetic tree, as shown in Section 2, "Nucleotide Frequency and Conservation Information" and in Table 2. These sequences have been aligned and analyzed with several covariation algorithms, as described in more detail in the "Predicting RNA Structure with Comparative Methods" section of the CRW Site http://www.rna.icmb.utexas.edu/METHODS/and in Section 2A.
These two regions could not be well aligned and we could not predict a common structure with comparative analysis with ten Eucaryotic sequences in 1988 (see Figures 35-43 in [ 48 ] ). However, once a larger number of related Eucaryotic 23S-like rRNA sequences was determined, we reanalyzed these two regions and were able to align those regions to other related organisms ( e.g., S. cerevisiae with Schizosaccharomyces pombe, Cryptococcus neoformans, Pneumocystis carinii, Candida albicans, and Mucor racemosus ) and predict a secondary structure that is common for all of these rRNAs (see Figures 3and 6 in [ 52 ] ). While the secondary structures for the fungal 23S-like rRNAs are determined in these regions, the animal rRNAs were only partially solved.
Sequences were aligned using Clustal X [ 28 ] and each alignment was visually inspected.
All complete CYTH domain sequences were aligned using the T_Coffee program, and this alignment was further refined based on the PSI-BLAST HSPs, conserved motifs detected in the Gibbs sampling procedure and predicted secondary structure for the individual groups (Fig.
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