Calibrating E-values for hidden Markov models with reverse-sequence null models

Calibrating E-values for hidden Markov models with reverse-sequence null models (2005)

Cached

Download Links

by Kevin Karplus , Rachel Karchin , George Shackelford , Richard Hughey

Venue:	Bioinformatics
Citations:	7 - 3 self

BibTeX

@ARTICLE{Karplus05calibratinge-values,
    author = {Kevin Karplus and Rachel Karchin and George Shackelford and Richard Hughey},
    title = {Calibrating E-values for hidden Markov models with reverse-sequence null models},
    journal = {Bioinformatics},
    year = {2005},
    pages = {4107--4115}
}

Bookmark

OpenURL

Abstract

Motivation: Hidden Markov models (hmms) calculate the probability that a sequence was generated by a given model. Log-odds scoring provides a context for evaluating this probability, by considering it in relation to a null hypothesis. We have found that using a reverse-sequence null model effectively removes biases due to sequence length and composition and reduces the number of false positives in a database search. Any scoring system is an arbitrary measure of the quality of database matches. Significance estimates of scores are essential, because they eliminate model- and methoddependent

Citations

1923	Basic local alignment search tool - Altschul, Gish, et al. - 1990
1891	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs - Altschul, Madden, et al. - 1997
703	SCOP: a Structural Classification Of Proteins database for the investigation of sequences and structures - Murzin, Brenner, et al. - 1995
671	Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features - Kabsch, Sander - 1983
547	Numerical Recipes - Press, Flannery, et al. - 1986
436	Hidden Markov models in computational biology. Applications to protein modeling - Krogh, Brown, et al. - 1994
229	Hughey R: Hidden Markov models for detecting remote protein homologies. Bioinformatics - Karplus, Barrett - 1998
131	A: Hidden Markov models for sequence analysis: Extension and analysis of the basic method - Hughey, Krogh - 1996
128	Hidden Markov models of biological primary sequence information - Baldi, Chauvin, et al. - 1994
116	Amino acid substitution matrices from an information theoretic perspective - Altschul - 1991
110	Multiple alignment using hidden markov models - Eddy - 1995
75	Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements - Schäffer, Aravind, et al. - 2001
63	Maximum discrimination hidden Markov models of sequence consensus - Eddy, Mitchison, et al. - 1995
63	Comparison of biosequences - Smith, Waterman - 2005
54	Meta-MEME: motif-based hidden Markov models of protein families - Grundy, Bailey, et al. - 1997
51	Protein modeling using hidden Markov models: Analysis of globins - Haussler, Krogh, et al. - 1993
46	Predicting protein structure using hidden Markov models. Proteins suppl - Karplus, Sjolander, et al. - 1997
43	protein structure using only sequence information. Proteins - Karplus, Barrett, et al. - 1999
42	What is the value added by human intervention in protein structure prediction? Proteins (Supplement 5): 86–91 - Karplus, Karchin, et al. - 2001
35	A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation - Bucher, Bairoch - 1994
35	Combining local-structure, fold-recognition, and new fold methods for protein structure prediction - Karplus, Karchin, et al. - 2003
32	Identification of protein sequence homology by consensus template alignment - Taylor - 1986
31	Scoring hidden Markov models - Barrett, Hughey, et al. - 1997
24	Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry - Karchin, Cline, et al. - 2003
23	A flexible motif search technique based on generalized profiles - Bucher, Karplus, et al. - 1996
23	Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks - Brevern, Etchebest, et al. - 2000
23	SAM: sequence alignment and modeling software system - Hughey, Karplus, et al. - 1999
17	Weighting hidden Markov models for maximum discrimination - Karchin, Hughey - 1998
14	Evaluation of local structure alphabets based on residue burial - Karchin, Cline, et al. - 2004
14	Statistical significance of probabilistic sequence alignment and related local hidden Markov models - Yu, Hwa - 2001
10	Parameterization studies for the SAM and HMMER methods of hidden Markov model generation - McClure, Smith, et al. - 1996
8	Estimating and evaluating the statistics of gapped local-alignment scores - Bailey, Gribskov - 2002
8	Library of routines for cumulative distribution functions, inverses, and other parameters - Brown, Lovato, et al. - 1997
2	Culling the PDB by resolution and sequence identity. http://www.fccc.edu/research/labs/dunbrack/pisces/ culledpdb.html - Wang, Dunbrack - 2003
1	gen sequence: an open-source library. http://www.soe.ucsc.edu/research/ compbio/gen sequence - Karplus - 2000