Computational Biology
Contents |
Multidotter
Multidotter is a dot-matrix program that is able to compare three or more sequences. As a result, Multidotter is able to identify conserved regions shared between as many sequences used as input. The display is still a two dimensional image with the axis corresponding to the first two input sequences and the conserved regions for all sequences superimposed on this image using different colours to highlight them. It becomes immediately possible to interpret those regions that are evolutionary or functionally conserved between all sequences.
References
If you use this tool, please cite:
- Y Nozaki, A Macgregor, C Smith, A Hunter and M Bellgard, Multidotter: Dot-Matrix Program for Multiple Sequences, The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'05) June 20-23, 2005, Las Vegas, USA.
If you have any questions or encounter problems, please do not hesitate to contact me at mbellgard@ccg.murdoch.edu.au
Sank AL
SANK_AL is an alignment tool for a pair of two sequences. The most significant feature of this program is to allow you to assign a priori the number of allowable gaps, rather than using an affine gap penalty that most other pairwise alignment programs employ. As a result, SANK_AL does not need to explore gap penalty parameter space, and has the potential to generate "biologically correct" or "acceptable" alignments, especially for short sequences (< 133 residues) with low similarity (<25%).
SANK_AL generates more than one alignment for any given pair of sequences
For a priori set of the maximal allowable gaps k, SANK_AL produces k+1 alignments with the best score with at most n gaps (n = 0,1, 2, ... , k). A statistical significance score of the alignment (P-value) suggests the optimal or near-optimal number of gaps. In the majority of cases, a minimal P-value associates with the correct biological alignment for a given number of allowable gaps.
References
- Nozaki, Y. and Bellgard, M. Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties. Bioinformatics. 2004 Dec 10; [Epub ahead of print]
- Bellgard, M., Gamble, T., Reynolds, M., Hunter, A., Trifonov, E., and Taplin. R. Gap mapping: a paradigm for aligning two sequences. Appl Bioinformatics. 2003;2(3 Suppl):S31-5.
If you have any questions or encounter problems, please contact mbellgard@ccg.murdoch.edu.au
