Table of Contents
What is a profile HMM and how is it used?
Because a profile HMM can serve as a representation of a sequence family or sequence domain, the most common application is to compare profile HMMs and sequences. These types of comparisons are more likely to identify distant homologs than sequence vs. sequence comparisons used in most database search programs.
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.
Profile hidden Markov models (HMMs) have several advantages over standard profiles. Profile HMMs have a formal probabilistic basis and have a consistant theory behind gap and insertion scores, in contrast to standard profile methods which use heuristic methods.
How do you align a sequence to an HMM?
Aligning a sequence to a profile HMM is done by a dynamic programming algorithm that finds the most probable path that the sequence may take through the model, using the transition and emissions probabilities to score each possible path.