Hidden Markov model-based method

Recently, a hidden Markov model-based method was developed to identify LOH from tumor samples alone, taking into account SNP intermarker distances, SNP-specific heterozygosity rates, and the haplofype structure of the human genome (31) to filter out false-positive LOH. When both parents share the same haplofype, the children will inherit a long stretch of homozygous geneotypes (32). 

The parsing of the transporter sequences into the TM domains shown in Fig. 1A represents the consensus result of three different methods. Average hydrophobicity was calculated with ProperTM using different window sizes and the Kyte and Doolittle scale (7). TMHMM, a hidden Markov model-based approach (8), and PHDHTM, a profile-based neural network method (9), were then utilized to refine the predictions. 

For these reasons, it is important to focus on the most divergent set of superfamily members that can be identified. Although a variety of new methods have recently been developed for identification of distantly related protein sequences [see, for example, Psi-Blast (Altschul et al, 1997), methods based on Hidden Markov Models such as SAMT98 (Kar-plus et al., 1998), the Intermediate Sequence Search algorithm of Park et al., (Park et al., 1997), or the simple congruence method, Shotgun (Pegg and Babbitt, 1999)], confirmation of these relationships can be technically difficult. In some cases, three-dimensional structural information or experimental structure-function analysis will be required to pro-... 

Other variations often appear utilizing different methodologies, but with no relative gain in accuracy. Those include methods that are based on hidden Markov models (Sasagawa and Tagima, 1993), stereo-chemical principles (Lim, 1974) and statistical mechanics (Ptitsyn and Finkelstein, 1983), just to cite a few. 

Other successful structure prediction methods based on sequence alone are FASTA [15, 18], hidden Markov models (HMMs) [25, 26, 28, 179], intermediate sequence search [182], and iterative profile search [29]. Sequence analysis methods are discussed in detail in Chapter 2. The results of such methods in the CASP experiment are described in [157, 183, 184],... 

Tobon-Mejia, DA., K. Medjaher, N. Zerhouni, G. Tripot (2012). A data-driven failure prognostics method based on mixture of gaussians hidden markov models. Reliability, IEEE Transactions on 61(2), 491-503. 

---