A comparison of profile hidden Markov model procedures for remote homology detection.

By Martin Madera, Julian Gough. 2002

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Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

Hidden Markov model speed heuristic and iterative HMM search procedure (2010, methodology): “5 database filtered for 40% identity [5,11-13].”
Accelerated Profile HMM Searches (2011, methodology): “Empirically too, any danger has seemed negligible, because profmark benchmarks tend to be broadly concordant with other published benchmarks [28,44].”
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress (2007, methodology): “MADS-box sequences available for all land plants were downloaded from SWISSPROT and TrEMBL [63] and their HMM profile was generated using HMMER 2.1.1 software package [64, 65 ].”
Structural bioinformatics A machine learning information retrieval approach to protein fold recognition (2006, unknown): “Profile–profile alignment approaches (Thompson et al., 1994; Rychlewski et al., 2000; Notredame et al., 2000; Yona and Levitt, 2002; Madera and Gough, 2002; Mitelman et al., 2003; Ginalski et al., 2003b; Sadreyev and Grishin, 2003; Edgar and Sjolander, 2003, 2004; Ohlson et al., 2004; Wallner et…”
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation (2008, background): “Other prior work has argued that HMMER scores do not follow expected Gumbel statistics [49], but HMMER2’s default mode is multihit glocal, not local (local alignment requires a command line option).”
Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models (2012, methodology): “HMM profiles are similar to PSI-BLAST profiles except they are applied within a more rigorous statistical framework and have been shown to perform considerably better when detecting distant relationships between homologous sequences [Madera and Gough, 2002].”
Alignment of protein sequences by their profiles (2004, methodology): “A particularly successful method in this class is implemented in the SAM package (Hughey and Krogh 1996) that outperforms other sequence-based methods for fold recognition (Karplus et al. 1998; Park et al. 1998; Madera and Gough 2002).”