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R Durbin

Publications and source records attributed to R Durbin.

17 recordsLinked to original sources
PubMed1995

Comparative sequence analysis of the human and pufferfish Huntington's disease genes.

The Huntington's disease (HD) gene encodes a novel protein with as yet no known function. In order to identify the functionally important domains of this protein, we have cloned and sequenced the homologue of the HD gene in the pufferfish, Fugu rubripes. The Fugu HD gene spans only 23 kb of genomic DNA, compared to the 170 kb human gene, and yet all 67 exons are conserved. The first coding exon, the site of the disease-causing triplet repeat, is highly conserved. However, the glutamine repeat in Fugu consists of just four residues. We also show that gene order may be conserved over longer stretches of the two genomes. Our work describes a detailed example of sequence comparison between human and Fugu, and illustrates the power of the pufferfish genome as a model system in the analysis of human genes.

Amino Acid Sequence↗
PubMed1995

Method for calculation of probability of matching a bounded regular expression in a random data string.

A method is presented for determining within strict bounds the probability of matching a regular expression with a match start point in a given section of a random data string. The method in general requires time and space exponential in the number of optional characters in the regular expression, but in practice was used to determine bounds for probabilities of matching all the ProSite patterns without difficulty.

Algorithms↗
PubMed1995

Maximum discrimination hidden Markov models of sequence consensus.

We introduce a maximum discrimination method for building hidden Markov models (HMMs) of protein or nucleic acid primary sequence consensus. The method compensates for biased representation in sequence data sets, superseding the need for sequence weighting methods. Maximum discrimination HMMs are more sensitive for detecting distant sequence homologs than various other HMM methods or BLAST when tested on globin and protein kinase catalytic domain sequences.

Algorithms↗
PubMed1994

RNA sequence analysis using covariance models.

We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences.

Algorithms↗
PubMed1994

A workbench for large-scale sequence homology analysis.

When routinely analysing very long stretches of DNA sequences produced by genome sequencing projects, detailed analysis of database search results becomes exceedingly time consuming. To reduce the tedious browsing of large quantities of protein similarities, two programs, MSPcrunch and Blixem, were developed, which assist in processing the results from the database search programs in the BLAST suite. MSPcrunch removes biased composition and redundant matches while keeping weak matches that are consistent with a larger gapped alignment. This makes BLAST searching in practice more sensitive and reduces the risk of overlooking distant similarities. Blixem is a multiple sequence alignment viewer for X-windows which makes it significantly easier to scan and evaluate the matches ratified by MSPcrunch. In Blixem, matches to the translated DNA query sequence are simultaneously aligned in three frames. Also, the distribution of matches over the whole DNA query is displayed. Examples of usage are drawn from 36 C. elegans cosmid clones totalling 1.2 megabases, to which these tools were applied.

Algorithms↗
PubMed1994

An expert system for processing sequence homology data.

When confronted with the task of finding homology to large numbers of sequences, database searching tools such as Blast and Fasta generate prohibitively large amounts of information. An automatic way of making most of the decisions a trained sequence analyst would make was developed by means of a rule-based expert system combined with an algorithm to avoid non-informative biased residue composition matches. The results found relevant by the system are presented in a very concise and clear way, so that the homology can be assessed with minimum effort. The expert system, HSPcrunch, was implemented to process the output to the programs in the BLAST suite. HSPcrunch embodies rules on detecting distant similarities when pairs of weak matches are consistent with a larger gapped alignment, i.e. when Blast has broken a longer gapped alignment up into smaller ungapped ones. This way, more distant similarities can be detected with no or little side-effects of more spurious matches. The rules for how small the gaps must be to be considered significant have been derived empirically. Currently a set of rules are used that operate on two different scoring levels, one for very weak matches that have very small gaps and one for medium weak matches that have slightly larger gaps. This set of rules proved to be robust for most cases and gives high fidelity separation between real homologies and spurious matches. One of the most important rules for reducing the amount of output is to limit the number of overlapping matches to the same region of the query sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1992

A survey of expressed genes in Caenorhabditis elegans.

As an adjunct to the genomic sequencing of Caenorhabditis elegans, we have investigated a representative cDNA library of 1,517 clones. A single sequence read has been obtained from the 5' end of each clone, allowing its characterization with respect to the public databases, and the clones are being localized on the genome map. The result is the identification of about 1,200 of the estimated 15,000 genes of C. elegans. More than 30% of the inferred protein sequences have significant similarity to existing sequences in the databases, providing a route towards in vivo analysis of known genes in the nematode. These clones also provide material for assessing the accuracy of predicted exons and splicing patterns and will lead to a more accurate estimate of the total number of genes in the organism than has hitherto been available.

Animals↗
PubMed1992

Transfection of a glycosylated phosphatidylinositol-anchored folate-binding protein complementary DNA provides cells with the ability to survive in low folate medium.

KB cells express a folate-binding protein that is anchored to the plasma membrane by a glycosylated phosphatidylinositol (GPI) tail and these cells can grow in medium containing a very low folate concentration (1 nM). In contrast, mouse 3T3 cells do not express a membrane-associated folate-binding protein and cannot grow under similar low folate conditions. In these studies, 3T3 cells were transfected with a vector containing the cDNA that codes for the KB cell folate-binding protein. In contrast to the wild-type 3T3 cells, the transfected 3T3 cells express a level of folate-binding protein similar to KB cells, 1 and 1.4 ng/micrograms protein, respectively. The capacity for binding [3H] folate to the surface of transfected 3T3 cells cultured in folate-deficient medium is 7.7 pmol/10(6) cells, and this is approximately 50% of the surface binding capacity of KG cells under similar culture conditions. Moreover, after treatment of the transfected 3T3 cells with phospholipase C specific for phosphatidylinositol, the binding of [3H] folate to the surface of these cells is reduced by 90%, indicating that, like the KB cells, the folate-binding protein is anchored to the plasma membrane by a GPI tail. Although the doubling time of wild-type 3T3 cells markedly increases after 13 d of culture in folate-deficient medium, the doubling time of both the transfected 3T3 cells and KB cells do not change. The results of these experiments indicate that the GPI-anchored folate-binding protein provides a mechanism to maintain a level of folate that permits the folate-dependent metabolic functions necessary for cell survival under low folate conditions.

3T3 Cells↗
PubMed1991

A mutant of Sindbis virus with altered plaque morphology and a decreased ratio of 26 S:49 S RNA synthesis in mosquito cells.

When our stock of standard Sindbis virus (SVSTD) is assayed by plaque formation on Aedes albopictus mosquito cells, about 1-2% of the plaques appear much clearer and sharper than the majority of the plaques. One of these clear plaques was picked, grown into a viral stock (SVCP), and used to prepare viral cDNA. Making use of the infectious Sindbis virus plasmid, Toto 1101 (Rice et al., 1987), we mapped the causal mutation for the clear plaque phenotype to a region between nt 7334 and 7716, and by sequencing of the viral RNA identified a mutation at nucleotide 7592. This mutation lies in the junction region of the viral genome, specifically at nucleotide -6, with reference to the initiation site for 26 S RNA synthesis. In SVCP-infected mosquito cells, but not in SVCP-infected chick cells, the ratio of subgenomic 26 S to 49 S (genomic) RNA synthesis was decreased relative to that observed in SVSTD infected cells. In terms of amino acid coding, the SVCP mutation is silent.

Aedes↗
PubMed1990

A dimension reduction framework for understanding cortical maps.

We argue that cortical maps, such as those for ocular dominance, orientation and retinotopic position in primary visual cortex, can be understood in terms of dimension-reducing mappings from many-dimensional parameter spaces to the surface of the cortex. The goal of these mappings is to preserve as far as possible neighbourhood relations in parameter space so that local computations in parameter space can be performed locally in the cortex. We have found that, in a simple case, certain self-organizing models generate maps that are near-optimally local, in the sense that they come close to minimizing the neuronal wiring required for local operations. When these self-organizing models are applied to the task of simultaneously mapping retinotopic position and orientation, they produce maps with orientation vortices resembling those produced in primary visual cortex. This approach also yields a new prediction, which is that the mapping of position in visual cortex will be distorted in the orientation fracture zones.

Animals↗
PubMed1989

Association of the Sindbis virus RNA methyltransferase activity with the nonstructural protein nsP1.

SVLM21 is a mutant of Sindbis virus, which in contrast to SVSTD, is able to replicate in Aedes albopictus mosquito cells deprived of methionine. We have obtained evidence that the basis of this low methionine-resistance (LMR) phenotype is the generation of an altered RNA methyltransferase with an increased affinity for S-adenosylmethionine (ado met). We now report that following the substitution of the nucleotide sequence, 126-504, from SVLM21 cDNA for the corresponding sequence of the Toto 1101 plasmid (infectious Sindbis viral RNA can be transcribed from this plasmid) we were able to generate recombinant Sindbis virus (SVMS-65a) with the LMR phenotype. (SVTOTO virus derived from Toto 1101, like SVSTD, lacks the LMR phenotype.) As was the case with SVLM21, SVMS-65a not only possessed the LMR phenotype but also showed an increased sensitivity to Neplanocin A, a potent inhibitor of S-adenosylhomocysteine (ado hcy) hydrolase. Sequencing of the nucleotide 126-504 region from SVLM21 revealed two mutations; these mutations occurred in adjacent codons and lead to two predicted amino acid changes in the SV nsPl protein; at residue 87, from Arg to Leu, and at residue 88 from Ser to Cys. Since the nucleotide sequence 126-504 lies entirely within the gene for nsP1, we conclude that the RNA methyltransferase activity generated by SV is associated with nsP1. We suggest that residues 87 and 88 in nsP1, where the amino acid changes in SVLM21 nsP1 have occurred, are at or near the binding site for ado met; we also suggest that these changes in nsP1 are responsible for the increased affinity of the SVLM21 RNA methyltransferase for ado met and thereby for the LMR phenotype. Alternatively, it is possible that the binding site for ado met is elsewhere on nsP1 or even on another protein, and that the changes at residues 87 and 88 lead to an alteration of the binding site.

Animals↗
PubMed1989

Image analysis of restriction enzyme fingerprint autoradiograms.

A genome mapping system has been developed that reads and assembles data from clones analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. Input data for the system can be most effectively obtained by the use of a scanning densitometer and image-processing package, such as that described in this article. The image-processing procedure involves preliminary location of bands, cooperative tracking of lanes by correlation of adjacent bands, a precise densitometric pass, alignment of the marker bands with the standard, optional interactive editing, and normalization of the accepted bands.

Animals↗
PubMed1988

Software for genome mapping by fingerprinting techniques.

A genome mapping package has been developed for reading and assembling data from clones analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. The package comprises: data entry; matching; assembly; statistical analysis; modelling. Data entry can be either manual or by a semiautomatic system based on a scanning densitometer. The primary emphasis in the analytical routines is on flexibility and interactive convenience, so that the operator has full knowledge of and control over the growing map, but a variety of automatic options are included. The package continually grows to meet the needs of the Caenorhabditis project.

Base Sequence↗
PubMed1985

Is there a single pathway for the folding of a polypeptide chain?

We argue that folding of the compact domains of proteins can occur with adequate rapidity in the absence of a unique directed mechanism, provided that native-like local structure dominates the folding process. We further suggest that the evolution of amino acid sequences should favor multiple paths to the folded state. Existing physicochemical and mutational data are not inconsistent with a many-pathway model. The analogy of a jigsaw puzzle, with multiple routes to a unique solution, appears to be particularly apt.

Amino Acid Sequence↗
PubMed1983

Monoclonal antibodies to three epitopic regions of feline leukemia virus p27 and their use in enzyme-linked immunosorbent assay of p27.

Three different monoclonal antibodies were developed against the major core protein (p27) of feline leukemia virus (FeLV). Each antibody was directed against a different epitope of the species-specific portion of FeLV-p27. The 3 antibodies reacted with 5 different isolates of FeLV but not with 7 other retroviruses (MuLV (Rauscher), MuLV (AKR), MPMV, MMTV, SMRV, BAEV, RD 114). These monoclonal antibodies could readily be adapted to an enzyme-linked immunosorbent assay (ELISA) for the specific measurement of FeLV-p27. When compared in an ELISA with conventional reagents, the battery of monoclonal antibodies proved to be as sensitive as conventional polyclonal antibodies.

Animals↗
PubMedDate not supplied

An analogue approach to the travelling salesman problem using an elastic net method.

The travelling salesman problem is a classical problem in the field of combinatorial optimization, concerned with efficient methods for maximizing or minimizing a function of many independent variables. Given the positions of N cities, which in the simplest case lie in the plane, what is the shortest closed tour in which each city can be visited once? We describe how a parallel analogue algorithm, derived from a formal model for the establishment of topographically ordered projections in the brain, can be applied to the travelling salesman problem. Using an iterative procedure, a circular closed path is gradually elongated non-uniformly until it eventually passes sufficiently near to all the cities to define a tour. This produces shorter tour lengths than another recent parallel analogue algorithm, scales well with the size of the problem, and is naturally extendable to a large class of optimization problems involving topographic mappings between geometrical structures.

Algorithms↗