ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.1

年代:1994

数据来源: MAL

摘要:

ABSTRACTWe have developed a general system, QGB, for performing complex queries on the information in the DDBJ/EMBL/GenBank databases, including queries over the structural features of sequences implied in the FEATURE TABLE. Queries are formed in a Structured Query Language (SQL)-like syntax with language extensions to support complex types (e.g., sets, ordered sets, and records) appropriate for representing and querying sequence data. A novel aspect of QGB is its ability to deduce missing features and infer relationships among features as a consequence of constructing a parse tree of sequence structure from information described in the FEATURE TABLE. The grammar for the parse tree is implemented in a customized form of the Definite Clause Grammar syntax of the logic programming language Prolog. The logic grammar formalism was chosen because it provides a perspicuous representation for features and constraints, and Prolog provides an execution model for the grammar rules. Construction of the parse tree also identifies inconsistencies and errors in the FEATURE TABLE that can in some cases be corrected automatically and used to generate an augmented version of the table.

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.3

年代:1994

数据来源: MAL

摘要:

ABSTRACTAutocrine ligands regulate important cell behavioral functions in both physiological and pathological conditions. Binding of these ligands to cell-surface receptors involves more subtle considerations than that of exogenous (endocrine or paracrine) ligands. Autocrine secretion leads to a release of molecules in the local microenvironment proximal to the cell surface, thus allowing interaction with receptors to compete directly with diffusive loss to the bulk extracellular medium. Complications in autocrine systems due to this bindingvs. transport competition arise in at least three aspects: (i) experimental measurement of autocrine ligand secretion rates is compromised; (ii) kinetics of autocrine ligand binding to cell-surface receptors are difficult to follow; and (iii) inhibition by exogenous blockers of autocrine ligand binding to cell receptors is problematic. At the heart of all these complications is the need to determine the fractional distribution of the secreted autocrine ligand between cell-surface receptor capture and diffusive loss to the bulk media. In this paper we offer a theoretical treatment of this problem using Brownian dynamics simulation techniques to calculate the capture probability of the cell receptors for the autocrine ligand. A major result is that the capture probability is significantly lower than the predicted by the Berg–Purcell steady-state diffusion approach. Another is that the capture probability is essentially independent of release location. Implications of these results for the complications found in autocrine systems are discusse

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.15

年代:1994

数据来源: MAL

摘要:

ABSTRACTWe have developed a two-level case-based reasoning architecture for predicting protein secondary structure. The central idea is to break the problem into two levels: (i) reasoning at the object (protein) level and using the global information from this level to focus on a more restricted problem space; (ii) decomposing objects into pieces (segments) and reasoning at the level of internal structures. As a last step to the procedure, inferences from the parts of the internal structure are synthesized into predictions about global structure. The architecture has been developed and tested on a commonly used data set with 69.5% predictive accuracy. It was then tested on a new data set with 68.2% accuracy. With additional tuning, over 70% accuracy was achieved. In addition, a series of experiments were conducted to test various aspects of the method and the results are informative.

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.25

年代:1994

数据来源: MAL

摘要:

ABSTRACTA computer program called BLASTX was previously shown to be effective in identifying and assigning putative function to likely protein coding regions by detecting significant similarity between a conceptually translated nucleotide query sequence and members of a protein sequence database. We present and assess the sensitivity of a new option to this software tool, herein called BLASTC, which employs information obtained from biases in codon utilization, along with the information obtained from sequence similarity. A rationale for combining these diverse information sources was derived, and analyses of the information available from codon utilization in several species were performed, with wide variation seen. Codon bias information was found on average to improve the sensitivity of detection of short coding regions of human origin by about a factor of 5. The implications of combining information sources on the interpretation of positive findings are discussed.

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.39

年代:1994

数据来源: MAL

摘要:

ABSTRACTThis paper presents an efficient method for constructing aligned blocks (i.e., gap-free multiple alignments) from a set of pairwise alignments. The method is more sensitive than some earlier block-constructing methods for detecting conserved sequence regions. The technique is applied to analyze conserved regions in protein prenyltransferases and to detect regulatory elements in the 5′ flank of the β-globin ge

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.51

年代:1994

数据来源: MAL

摘要:

ABSTRACTWe describe a conceptual model for genome databases that facilitates the process of building, maintaining, and disseminating physically anchored genetic linkage maps. The model has been implemented as a relational database at the Roman L. Hruska U.S. Meat Animal Research Center (MARC). Development of consensus maps using disparate data from different reference pedigrees or laboratories is supported. The model is of use to quantitative and population geneticists interested in loci that affect phenotypes and marker-assisted selection, and it is sufficiently flexible for centralized, species genome databases facilitating comparative mapping. The MARC genome database is used to assemble, maintain, and disseminate physically anchored genetic linkage maps for cattle, swine, and sheep currently based on more than 100,000 genotypes from 1,000 markers. Integrated with linkage analysis software, this database permits frequent updates of physically anchored genetic linkage maps.

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.65

年代:1994

数据来源: MAL

摘要:

ABSTRACTEvolutionary inference methods that assume equal DNA base compositions and symmetric nucleotide substitution matrices, where these assumptions do not hold, are likely to group species on the basis of similar base compositions rather than true phylogenetic relationships. We propose an invariants-based method for dealing with this problem. An invariant QTof a tree T under a k-state Markov model, where a generalized time parameter is identified with the E edges of T, allows us to recognize whether data on N observed species can be associated with the N terminal vertices of T in the sense of having been generated on T rather than on any other tree with N terminals. The form of the generalized time parameter is a positive determinant matrix in some semigroup S of stochastic matrices. The invariance is with respect to the choice of the set of E matrices in S, one associated with each of the E edges of T. We apply a general "empirical" method of finding invariants of a parametrized functional form. It involves calculating the probability f of all kNdata possibilities for each of m sets of E matrices in S to associate with the edges of T, then solving for the parameters using the m equations of form Q(f) = 0. We discuss the problems of finding asymmetric models satisfying the property of semigroup closure, of finding asymmetric models that admit invariants at all, and of the computational complexity of the method. We propose a class of semigroups Sccontaining matrices of form |1–a ca a 1–ca| to account for A+T versus G+C asymmetries in DNA base composition. Quadratic invariants are obtained for rooted trees with three and with four terminals. In the latter case the smallest set of algebraically independent invariants is sought. These invariants are applied to data pertaining the fungal evolution and to the origin of mitochondria as bacterial endosymbio

ISSN:1066-5277    

DOI:10.1089/cmb.1994.1.77

年代:1994

数据来源: MAL