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Hidden Markov models for detecting remote protein homologies
 Bioinformatics
, 1998
"... A new hidden Markov model method (SAMT98) for nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (hmm) from the sequence and homologs found using the hmm for database search. SAMT98 is ..."
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Cited by 409 (15 self)
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A new hidden Markov model method (SAMT98) for nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (hmm) from the sequence and homologs found using the hmm for database search. SAMT98 is also used to construct model libraries automatically from sequences in structural databases. We evaluate the SAMT98 method with four datasets. Three of the test sets are foldrecognition tests, where the correct answers are determined by structural similarity. The fourth uses a curated database. The method is compared against wublastp and against doubleblast, a twostep method similar to ISS, but using blast instead of fasta. Results SAMT98 had the fewest errors in all tests dramatically so for the foldrecognition tests. At the minimumerror point on the SCOPdomains test, SAMT98 got 880 true positives and 68 false positives, doubleblast got 533 true positives with 71 false positives, and wublastp got 353 true positives with 24 false positives. The method is optimized to recognize superfamilies, and would require parameter adjustment to be used to nd family or fold relationships. One key to the performance of the hmm method is a new scorenormalization technique that compares the score to the score with a reversed model rather than to a uniform null model. Availability A World Wide Web server, as well as information on obtaining the Sequence Alignment and PREPRINT to appear in Bioinformatics, 1999
Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology
, 1996
"... This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a protein family or domain are known. We present a method for condensing the information in a protein dat ..."
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Cited by 149 (24 self)
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This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a protein family or domain are known. We present a method for condensing the information in a protein database into a mixture of Dirichlet densities. These mixtures are designed to be combined with observed amino acid frequencies, to form estimates of expected amino acid probabilities at each position in a profile, hidden Markov model, or other statistical model. These estimates give a statistical model greater generalization capacity, such that remotely related family members can be more reliably recognized by the model. Dirichlet mixtures have been shown to outperform substitution matrices and other methods for computing these expected amino acid distributions in database search, resulting in fewer false positives and false negatives for the families tested. This paper corrects a previously p...
Recent improvements to the PROSITE database
 Nucleic Acids Research
, 2004
"... The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or pro®les. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identi®ed by the signature. Th ..."
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Cited by 99 (8 self)
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The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or pro®les. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identi®ed by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest
Scoring Hidden Markov Models
"... Motivation: Statistical sequence comparison techniques, such as hidden Markov models and generalized pro les, calculate the probability that a sequence was generated by a given model. Logodds scoring is a means of evaluating this probability by comparing it to a null hypothesis, usually a simpler s ..."
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Cited by 43 (5 self)
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Motivation: Statistical sequence comparison techniques, such as hidden Markov models and generalized pro les, calculate the probability that a sequence was generated by a given model. Logodds scoring is a means of evaluating this probability by comparing it to a null hypothesis, usually a simpler statistical model intended to represent the universe of sequences as a whole, rather than the group of interest. Such scoring leads to two immediate questions: what should the null model be, and what threshold of logodds score should be deemed a match to the model. Results: This paper experimentally analyses these two issues. Within the context of the Sequence Alignment and Modeling software suite (SAM), we consider a variety ofnull models and suitable thresholds. Additionally, we consider HMMer's logodds scoring and SAM's original Zscoring method. Among the null model choices, a simple looping null model that emits characters according to the geometric mean of the character probabilities in the columns modeled by the HMM performs well or best across all four discrimination experiments.
Grouping Web Page References into Transactions for Mining World Wide Web Browsing Patterns
 Dept. of Computer Science, Univ. of Minnesota
, 1997
"... Webbased organizations often generate and collect large volumes of data in their daily operations. Analyzing such data involves the discovery of meaningful relationships from a large collection of primarily unstructured data, often stored in Web server access logs. While traditional domains for dat ..."
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Cited by 38 (3 self)
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Webbased organizations often generate and collect large volumes of data in their daily operations. Analyzing such data involves the discovery of meaningful relationships from a large collection of primarily unstructured data, often stored in Web server access logs. While traditional domains for data mining, such as point of sale databases, have naturally defined transactions, there is no convenient method of clustering web references into transactions. This paper identifies a model of user browsing behavior that separates web page references into those made for navigation purposes and those for information content purposes. A transaction identification method based on the browsing model is defined and successfully tested against other methods, such as the maximal forward reference algorithm proposed in [1]. Transactions identified by the proposed methods are used to discover association rules from real world data using the WEBMINER system [7]. 1 Introduction and Background As more or...
Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models
 J. COMP. BIOL
, 2001
"... The score statistics of probabilistic gapped local alignment of random sequences is investigated both analytically and numerically. The full probabilistic algorithm (e.g., the “local” version of maximumlikelihood or hidden Markov model method) is found to have anomalous statistics. A modified “semi ..."
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Cited by 18 (3 self)
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The score statistics of probabilistic gapped local alignment of random sequences is investigated both analytically and numerically. The full probabilistic algorithm (e.g., the “local” version of maximumlikelihood or hidden Markov model method) is found to have anomalous statistics. A modified “semiprobabilistic” alignment consisting of a hybrid of Smith–Waterman and probabilistic alignment is then proposed and studied in detail. It is predicted that the score statistics of the hybrid algorithm is of the Gumbel universal form, with the key Gumbel parameter l taking on a fixed asymptotic value for a wide variety of scoring systems and parameters. A simple recipe for the computation of the “relative entropy,” and from it the finite size correction to l, is also given. These predictions compare well with direct numerical simulations for sequences of lengths between 100 and 1,000 examined using various PAM substitution scores and affine gap functions. The sensitivity of the hybrid method in the detection of sequence homology is also studied using correlated sequences generated from toy mutation models. It is found to be comparable to that of the Smith–Waterman alignment and significantly better than the Viterbi version of the probabilistic alignment.
Epalinges/s Lausanne
"... The simultaneous alignment of three or more nucleotide or amino acid sequences is one of the commonest tasks in bioinformatics. Multiple alignments are an essential prerequisite to many ..."
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The simultaneous alignment of three or more nucleotide or amino acid sequences is one of the commonest tasks in bioinformatics. Multiple alignments are an essential prerequisite to many