MAMOT -- hidden MArkov MOdelling Tool
What you can do:
Predict features in biological sequences.
Highlights:
- MAMOT is a command-line program for Unix-like operating systems, including MacOS X, that was developed to allow scientists to apply HMMs more easily in their research.
- One can define the architecture and initial parameters of the model in a text file and then use MAMOT for parameter optimization on example data, decoding (like predicting motif occurrence in sequences) and the production of stochastic sequences generated according to the probabilistic model.
- Two examples for which models are provided are coiled-coil domains in protein sequences and protein binding sites in DNA.
- Features include the use of pseudocounts, state tying and fixing of selected parameters in learning, and the inclusion of prior probabilities in decoding.
Keywords:
- hidden Markov model
- sequence analysis
- RNA sequence
- DNA sequence
- protein sequence
- amino acid sequence
Literature & Tutorials:
PubMed Link: MAMOT: hidden Markov modeling tool
This record last updated: 01-11-2010