An HMM posterior decoder for sequence feature prediction that includes homology information
نویسندگان
چکیده
منابع مشابه
An HMM posterior decoder for sequence feature prediction that includes homology information
MOTIVATION When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. RESULTS We present here a general hidden Markov model (HMM) decoding algorithm that combines probabilities for sequence features of homologs by considering the average of the posterior label probabilit...
متن کاملProtein homology detection by HMM–HMM comparison
Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and
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MOTIVATION Much information about new protein sequences is derived from identifying homologous proteins. Such tasks are difficult when the evolutionary relationships are distant. Some modern methods achieve better results by building a model of a set of related sequences, and then identifying new proteins that fit the model. A further advance was the development of iterative methods that refine...
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MOTIVATION Identifying residues that interact with ligands is useful as a first step to understanding protein function and as an aid to designing small molecules that target the protein for interaction. Several studies have shown that sequence features are very informative for this type of prediction, while structure features have also been useful when structure is available. We develop a seque...
متن کاملSequence context-specific profiles for homology searching: Supplementary Information
Generation of context profile library N = 1 million training profiles of length l = 2d+1 were generated as described in the main text and Figure 2. Each training profile is represented by a count profile cn(j, x), which specifies the counts of amino acid x ∈ {1, . . . , 20} at position j ∈ {−d, . . . , d}. These counts are obtained by multiplying the sequence profile tn(j, x) by the effective n...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2005
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bti1014