Last modified on 25 January 2016.

Literature Reference:

Shang L., Gardner D.P., Xu W., Cannone J.J., Miranker D.P., Ozer S., and Gutell R.R. (2013).
Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems.
BMC Systems Biology, 7(S4):S13.
[ pm | pmc | DOI ]

Manuscript Figures and Table:

Description Figure
Figure 1: Example of the alignment statistics generation process performed by CRWAlign:
  1. 10 template sequences (red - bacillales, blue - bacilli, brown - bacteria) are used to determine conserved alignment columns;
  2. computation of the average block 5 score for the bacilli node.
 PNG
Figure 2: Example of the alignment process performed by CRWAlign:
  1. unaligned RNA sequences;
  2. 3 bacillales (red) template sequences and average block scores;
  3. single match is found for block 5 is aligned;
  4. 3 matches are found for block 3;
  5. no matches are found for block 5;
  6. 7 template sequences (red - bacillales, blue - bacilli) and average block scores;
  7. a match is found for block 5.
 PNG
Figure 3: The relationship between structural elements (a) and the template sequence alignment (b), which affects the structural descriptor generation (c). PNG
Figure 4: The flowchart of the complete structural model identification process. PNG
Figure 5: Pairwise sequence accuracy results from alignment of 1,000 bacterial 16S rRNA sequences for ten alignment programs. PNG
Figure 6: Pairwise sequence accuracy results from alignment of 1,000 bacterial 16S rRNA sequences for four alignment programs and three different template alignments (250, 500 and 2,000 sequences). PNG
Figure 7: Execution time for aligning 1,000 bacterial 16S rRNA sequences for five alignment programs. PNG
Figure 8: Execution time for the different phases of the a) CRWAlign-1 and b) CRWAlign-2 programs when aligning 500 and 1,000 bacterial 16S rRNA sequences and using 250, 500 and 2000 template sequences. PNG
Table 1: Sequences in template alignments and used for testing. No overlap occurs between sequences tested and sequences in template alignments. HTML