HPC Module: PROBCONS
Synopsis
Adds PROBCONS software to your environment.
| About This Software | |
|---|---|
| Official Site | http://probcons.stanford.edu |
| Tags | Multiple Sequence Alignment |
Installed Versions
| Version | Install Date | Default? |
|---|---|---|
| 1.12 | 2016-04-01 |
Description
The basis for the PROBCONS algorithm is the computation of pairwise posterior probability matrices, P(xi ~ yj | x, y), which give the probability that one should match letters xi and yj when aligning two sequences x and y. PROBCONS uses a simple probabilistic model that allows for efficient computation of these probabilities. Given these posterior matrices, PROBCONS applies the probabilistic consistency transformation to incorporate evidence from intermediate sequences. Finally, PROBCONS performs progressive alignment using a sum-of-pairs maximum expected accuracy objective function.
Because of the algorithm, Probcons is best suited for a smaller number of sequences >1000. When getting over this number the amount of time needed for alignment can be drastically increased.
Citation(s)
PROBCONS is discussed in the following papers:
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Do, C.B., Brudno, M., and Batzoglou, S. 2004. PROBCONS: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. To appear in ISMB.
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Do, C.B., Brudno, M., and Batzoglou, S. 2004. ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. To appear in AAAI.
Category
| Library | Programming | Software | SysAdmin |
|---|---|---|---|