Biomedical subjects

T I Dix

Publications and source records attributed to T I Dix.

6 recordsLinked to original sources

PubMed1998

Discovering simple DNA sequences by compression.

An information-theoretic DNA compression scheme devised by Milosavljevic and Jurka (1993) has been used in many places in the literature for both the discovery of new genes and the compression of DNA. Their compression method applies an encoding of previously occurring runs. They use 5 different code-words: four being the DNA bases, A, C, G and T, and the other being a pointer to a previously occurring run. They advocate a code-word of length log2 5 for each of these and then encoding a run by a code-word of length 2 x log2 n, where n is the length of the sequence. This scheme encodes the start of the sequence with a code-word of length log2 n and likewise encodes the end of the sequence with a code-word of length log2 n. In this paper, we show the above coding scheme to be inefficient in various ways and improve upon it so that it can compress DNA. We discuss our implementation of various schemes some of which run in linear time.

Algorithms↗

PubMed1998

Compression of strings with approximate repeats.

We describe a model for strings of characters that is loosely based on the Lempel Ziv model with the addition that a repeated substring can be an approximate match to the original substring; this is close to the situation of DNA, for example. Typically there are many explanations for a given string under the model, some optimal and many suboptimal. Rather than commit to one optimal explanation, we sum the probabilities over all explanations under the model because this gives the probability of the data under the model. The model has a small number of parameters and these can be estimated from the given string by an expectation-maximization (EM) algorithm. Each iteration of the EM algorithm takes O(n2) time and a few iterations are typically sufficient. O(n2) complexity is impractical for strings of more than a few tens of thousands of characters and a faster approximation algorithm is also given. The model is further extended to include approximate reverse complementary repeats when analyzing DNA strings. Tests include the recovery of parameter estimates from known sources and applications to real DNA strings.

Algorithms↗

PubMed1997

Comparison of clone-ordering algorithms used in physical mapping.

In this paper, a number of existing and novel techniques are considered for ordering cloned extracts from the genome of an organism based on fingerprinting data. A metric is defined for comparing the quality of the clone order for each technique. Simulated annealing is used in combination with several different objective functions. Empirical results with many simulated data sets for which the correct solution is known indicate that a simple greedy algorithm with some subsequent stochastic shuffling provides the best solution. Other techniques that attempt to weight comparisons between nonadjacent clones bias the ordering and give worse results. We show that this finding is not surprising since without detailed attempts to reconcile the data into a detailed map, only approximate maps can be obtained. Making N2 pieces of data from measurements of N clones cannot improve the situation.

Algorithms↗

PubMed1996

Circular clustering of protein dihedral angles by Minimum Message Length.

Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level classification which remains popular today. Using the Snob program for information-theoretic Minimum Message Length (MML) classification, we are able to take the protein dihedral angles as determined by X-ray crystallography, and cluster sets of dihedral angles into groups. Previous work by Hunter and States has applied a similar Bayesian classification method, AutoClass, to protein data with site position represented by 3 Cartesian co-ordinates for each of the alpha-Carbon, beta-Carbon and Nitrogen, totalling 9 co-ordinates. By using the von Mises circular distribution in the Snob program, we are instead able to represent local site properties by the two dihedral angles, phi and psi. Since each site can be modelled as having 2 degrees of freedom, this orientation-invariant dihedral angle representation of the data is more compact than that of nine highly-correlated Cartesian co-ordinates. Using the information-theoretic message length concepts discussed in the paper, such a more concise model is more likely to represent the underlying generating process from which the data came. We report on the results of our classification, plotting the classes in (phi, psi) space; and introducing a symmetric information-theoretic distance measure to build a minimum spanning tree between the classes. We also give a transition matrix between the classes and note the existence of three classes in the region phi approximately -1.09 rad and psi approximately -0.75 rad which are close on the spanning tree and have high inter-transition probabilities. This gives rise to a tight, abundant and self-perpetuating structure.

Computational Biology↗

PubMed1994

A restriction mapping engine using constraint logic programming.

Restriction mapping generally requires the application of information from various digestions by restriction enzymes to find solution sets. We use both the predicate calculus and constraint solving capabilities of CLP(R) to develop an engine for restriction mapping. Many of the techniques employed by biologists to manually find solutions are supported by the engine in a consistent manner. We provide generalized pipeline and cross-multiply operators for combining sub-maps. Our approach encourages the building of maps iteratively. We show how other techniques can be readily incorporated.

Animals↗

PubMed1988

Errors between sites in restriction site mapping.

Restriction site mapping programs construct maps by generating permutations of fragments and checking for consistency. Unfortunately many consistent maps often are obtained within the experimental error bounds, even though there is only one actual map. A particularly efficient algorithm is presented that aims to minimize error bounds between restriction sites. The method is generalized for linear and circular maps. The time complexity is derived and execution times are given for multiple enzymes and a range of error bounds.

Algorithms↗