Last modified on 25 January 2016.

Literature Reference:

Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
An Accurate Scalable Template-Based Alignment Algorithm.
Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
[ PM | PMC | DOI ]

Manuscript Figures:

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.
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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.
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Figure 3: Pairwise sequence accuracy results from
  1. alignment of 1000 bacterial 16S rRNA sequences for 9 alignment programs and
  2. alignment of 500 bacterial 23S rRNA sequences for 6 alignment programs.
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Figure 4: Pairwise sequence accuracy results from alignment of 1000 bacterial 16S rRNA sequences for 3 alignment programs and 3 different template alignments (250, 500 and 2000 sequences). PNG
Figure 5: Execution time for
  1. aligning 1000 bacterial 16S rRNA sequences for four alignment programs and
  2. the two phases of the CRWAlign programs when aligning 500 (red) and 1000 (black) bacterial 16S rRNA sequences and using 250, 500 and 2000 template sequences.
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