Table of Contents
What is HMM state?
In the hidden Markov models considered above, the state space of the hidden variables is discrete, while the observations themselves can either be discrete (typically generated from a categorical distribution) or continuous (typically from a Gaussian distribution).
What is HMM format?
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. Profile-HMMs are constructed from a multiple sequence alignment in the HMMER package using the hmmbuild program.
What is HMM topology?
An HMM topology is defined as the statistical behavior of an observable symbol sequence in terms of a network of states, which represents the overall process behavior with regard to movement between states of the process, and describes the inherent variations in the behavior of the observable symbols within a state.
How Kalman filter is different than Hmm?
The Kalman filter may be regarded as analogous to the hidden Markov model, with the difference that the hidden state variables have values in a continuous space as opposed to a discrete state space as for the hidden Markov model.
What is a profile HMM?
Profile HMMs. A profile HMM is a variant of an HMM relating specifically to biological sequences. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system, which can be used to align sequences and search databases for remotely homologous sequences.
What is a profile hidden Markov model (profile-HMM)?
One model that is especially useful for representing the profile of a multiple sequence alignment is the profile hidden Markov model (profile-HMM) [24, 25]. Profile-HMMs are HMMs with a specific architecture that is suitable for modeling sequence profiles.
How do I test the profile HMM alignment tool?
To test the profile HMM alignment tool you can re-align the sequences from the multiple alignment to the HMM model. First erase the periods in sequences used to format the downloaded aligned sequences. Doing this removes the alignment information from the sequences. Now align all the proteins to the HMM profile.
What are pair-HMMs and profile-cshmms?
In Sec. 4, we focus on pair-HMMs and their applications in pairwise alignment, multiple sequence alignment, and gene prediction. Section 5 reviews context-sensitive HMMs (csHMMs) and profile context-sensitive HMMs (profile-csHMMs), which are especially useful for representing RNA families.