SEARCH · PubMed Health

Results for “alignment chaining method”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources

PubMed2000

Altered gene expression in kidneys of mice with 2,8-dihydroxyadenine nephrolithiasis.

BACKGROUND: We have developed a knockout mouse model for adenine phosphoribosyltransferase (APRT) deficiency, a condition that often leads to 2,8-dihydroxyadenine (DHA) nephrolithiasis in humans. Aprt knockout male mice develop severe renal damage by three months of age, but this is strain specific. Renal damage in female mice is less pronounced than in males. The gene level changes that promote renal injury in APRT-deficient mice are not known. METHODS: We used mRNA differential display polymerase chain reaction (DD-PCR) to analyze renal gene expression changes in APRT-deficient male and female mice (strain C3H) compared with age- and sex-matched Aprt heterozygote controls. The differentially amplified bands were reamplified, cloned, sequenced, and queried against the National Center for Biotechnology Information nonredundant databases using the Basic Alignment Search Tool. Relative quantitative reverse transcription-polymerase chain reaction was used to confirm the results of DD-PCR for a selected number of genes in one-, three-, and six-month-old male and female mice. RESULTS: Sixty-three differentially amplified bands were identified, including 21 for known genes, and 8 of these were examined further. In three-month-old APRT-deficient male mice, the expression of C10 was increased tenfold, and there was a fourfold to sevenfold increase in the expression of a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS-1), MGP (matrix Gla protein), and lysyl oxidase (LOX). The expression of cholecystokinin-A receptor (CCKAR), imprinted multimembrane-spanning polyspecific transporter-like gene 1 (IMPT-1), and kidney androgen-regulated protein (KAP) was diminished twofold to fourfold, but there was little or no change in the expression of organic anion transporter (OATP). Except for a more than tenfold increase in C10 expression and up to tenfold decrease in KAP expression, APRT-deficient female mice did not show significant changes in gene expression compared with controls. CONCLUSIONS: These findings suggest that (1) there are sex-related differences in gene expression in DHA lithiasis, possibly caused by increased deposition of DHA crystals in male compared with female kidneys; and (2) the expression of certain genes (for example, C10) may simply be an indication of nonspecific cellular stimulation and may not be related to renal injury.

Adenine↗

PubMed1997

Evidence for recombination in the flagellin locus of Campylobacter jejuni: implications for the flagellin gene typing scheme.

The flagellin subunit of the flagellar filament in Campylobacter jejuni is encoded by two highly homologous tandem genes, flaA and flaB. The flaA gene was sequenced in 18 strains of C. jejuni, including isolates from three outbreak groups. Sequences obtained were compared with flaA sequences available in the GenBank database, and all were analyzed for mosaic gene structure by using recently described statistical tests for detecting gene conversion among aligned sets of sequences. Strong evidence was found supporting recombination between flaA genes of different strains (i.e., intergenomic recombination). Intragenomic recombination between the flaA and flaB genes of C. jejuni TGH9011 was also demonstrated. Both mechanisms of recombination may act as a potential means by which pathogenic strains can generate increased antigenic diversity, so allowing them to escape the immunological responses of the host. Furthermore, demonstration of recombination within and between flagellin loci of natural strains suggests that flagellin gene typing (restriction fragment length polymorphism analysis of PCR-amplified flagellin genes) cannot be considered a stable method for long-term monitoring of pathogenic Campylobacter populations.

Base Sequence↗

PubMed1997

Model building by comparison: a combination of expert knowledge and computer automation.

The CASP blinds trials (Critical Assessment of techniques for protein Structure Prediction) assess the accuracy of protein prediction that includes evaluation of comparative model building of protein structures. Comparative models of four proteins (T0001, T0003, T0017, and T0028) for CASP2 (held during 1996) were constructed using computer algorithms combined with visual inspection. Essentially the main-chain modelling involves construction of the target structure from rigid-body segments of homologues and loop fragments extracted from homologous and nonredundant databases. Side-chains were initially constructed by inheritance from the parent or from a rotamer library. Side-chain conformations were then refined using a novel mean field approach that includes solvation. Comparison of the models with the subsequently released X-ray structures identified the successes and limitations of our approach. The most problematic area is the quality of the sequence alignments between parent(s) and target. In this respect the overinterpretation of the conserved features within homologous families can be misleading. Several features of our approach have a positive effect on the accuracy of the models. For T0003, inspection correctly identified that a lower sequence identity parent provides the best framework for this model. Loop selection worked well where a homologous protein fragment was used, but that the use of nonredundant fragment library remains problematic for hinge movements and displacements in secondary structure elements relative to the parent. Side-chain refinement improved residue conformations relative to the initial model. Use of limited energy minimization improved the stereochemical quality of the model without increasing the RMS deviation. This study has identified methods that are effective and areas requiring further attention to improve model building by comparison.

Amino Acid Sequence↗

PubMed2005

Prediction of novel and analogous folds using fragment assembly and fold recognition.

A number of new and newly improved methods for predicting protein structure developed by the Jones-University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and "microdomain" folding in order to build complete chain models for some targets.

Algorithms↗

PubMedDate not supplied

Methods for studying transmembrane peptides in bicelles: consequences of hydrophobic mismatch and peptide sequence.

We have shown that bicelles prepared from dilauryl phosphatidylcholine (DLPC) and dipalmitoyl phosphatidylcholine (DPPC) align in a magnetic field under conditions similar to the more common dimyristoyl phosphatidylcholine (DMPC) bicelles. In addition, a model transmembrane peptide, P16, with a hydrophobic stretch of 24 A, and specific alanine-d(3) labels, was incorporated into all of the different bicelles. The long-chain phospholipid (DLPC, DMPC, or DPPC) remained unperturbed upon incorporation of the peptide while the quadrupolar splitting of the short-chain phospholipid along the bicelle rim increased by varying degrees in the different bicelle systems. The change in quadrupolar splitting of the short-chain phospholipids was attributed to changes in either fluidity of the planar region of the bicelle or differences in overall lipid packing. When the hydrophobic stretch of the bilayer was 22.8 (DMPC) or 26.3 A (DPPC), the peptide tilt was found to be transmembrane (33-35 degrees with respect to the bicelle normal). When the hydrophobic stretch of the bilayer was 19.5 A (DLPC), the peptide quadrupolar splittings suggested a loss of transmembrane orientation. When tryptophan was incorporated in the middle of the transmembrane region, the transmembrane orientation was also lost.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2001

Genetic characterization of six species of diplozoids (Monogenea; Diplozoidae).

The second internal transcribed spacer (ITS2) of the ribosomal RNA gene array of 6 species of diplozoids; Eudiplozoon nipponicum, Paradiplozoon bliccae, P. homoion, P. megan, P. pavlovskii and P. sapae, was amplified by PCR and sequenced. These sequences clearly demonstrate discrimination at the species level and confirm the validity of species determined by morphological identification. No intraspecific variation was found in the ITS2 sequences. There were no differences in the ITS2 sequences of P. homoion from populations parasitizing different host species. The length of the PCR product allowed discrimination of E. nipponicum from the Paradiplozoon species. Digestion of the amplified ITS2 fragment with enzymes AluI, HaeIII and HinfI provided useful genetic markers for species identification. The genetic relationships between diplozoids again demonstrated that E. nipponicum was the most genetically distinct species, whereas P. bliccae and P. sapae were the species most closely related. This represents the first molecular taxonomic study of these interesting parasites and demonstrates the utility of these methods for addressing questions of systematics.

Animals↗

PubMed2005

Assembly of highly aligned DNA strands onto Si chips.

This paper reports a robust and efficient approach to assemble highly aligned DNA strands onto Si chips. The method combines advantages from molecular combing and microcontact printing to realize controlling both the density and direction of DNA strands on the Si chip. In addition, it also can be utilized to prepare stretched DNA structures on solid surfaces. Compared to approaches that use molecular combing directly on silanated surfaces, the stretched single-chain DNA structures are straighter. Furthermore, by exploiting the hydrophobic property of the intrinsic poly(dimethylsiloxane) stamp, this study also describes a simple way to produce straight bundled DNA arrays on Si and other substrates.

Adsorption↗

PubMed2005

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.

We report here an advanced approach for the characterization of the folding pattern of a de novo designed antiparallel coiled coil peptide by high-resolution methods. Incorporation of two fluorescence labels at the C- and N-terminus of the peptide chain as well as modification of two hydrophobic core positions by Phe/[15N,13C]Leu enable the study of the folding characteristics and of distinct amino acid side chain interactions by fluorescence resonance energy transfer (FRET) and NMR spectroscopy. Results of both experiments reveal the antiparallel alignment of the helices and thus prove the design concept. This finding is also supported by molecular dynamics simulations. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in combination with NMR experiments was used for verification of the oligomerization equilibria of the coiled coil peptide.

Amino Acid Sequence↗

PubMed2000

Amblyopes see true alignment where normal observers see illusory tilt.

Amblyopia ("lazy eye") is an impairment in visual acuity resulting from abnormal neural development in the visual cortex. We tested the responses of ten amblyopic and six normal observers to illusions of perceived orientation in textures of Gabor patches: the "Fraser illusion," the "phase illusion," and a "tilted chain" illusion. The illusory tilt of the stimulus rows was matched by actual tilt in the opposite direction by using the method of constant stimuli. Amblyopes showed a significant increase in the Fraser illusion, a decrease in the phase illusion, and a reversal of the tilted chain illusion. Amblyopic performance could be simulated in normal observers by reducing the length of the rows. These results can be modeled by a theory which places the neural abnormality in amblyopia at the level of second stage grouping processes. Additionally, the illusions might be useful in the early diagnosis of amblyopia without the need for prior refractive correction.

Amblyopia↗

PubMed2001

Design of inhibitors of Ras--Raf interaction using a computational combinatorial algorithm.

Drugs that inhibit important protein-protein interactions are hard to find either by screening or rational design, at least so far. Most drugs on the market that target proteins today are therefore aimed at well-defined binding pockets in proteins. While computer-aided design is widely used to facilitate the drug discovery process for binding pockets, its application to the design of inhibitors that target the protein surface initially seems to be limited because of the increased complexity of the task. Previously, we had started to develop a computational combinatorial design approach based on the well-known 'multiple copy simultaneous search' (MCSS) procedure to tackle this problem. In order to identify sequence patterns of potential inhibitor peptides, a three-step procedure is employed: first, using MCSS, the locations of specific functional groups on the protein surface are identified; second, after constructing the peptide main chain based on the location of favorite locations of N-methylacetamide groups, functional groups corresponding to amino acid side chains are selected and connected to the main chain C(alpha) atoms; finally, the peptides generated in the second step are aligned and probabilities of amino acids at each position are calculated from the alignment scheme. Sequence patterns of potential inhibitors are determined based on the propensities of amino acids at each C(alpha) position. Here we report the optimization of inhibitor peptides using the sequence patterns determined by our method. Several short peptides derived from our prediction inhibit the Ras--Raf association in vitro in ELISA competition assays, radioassays and biosensor-based assays, demonstrating the feasibility of our approach. Consequently, our method provides an important step towards the development of novel anti-Ras agents and the structure-based design of inhibitors of protein--protein interactions.

Algorithms↗

PubMedDate not supplied

Identification of fungi based on the nucleotide sequence homology of their internal transcribed spacer 1 (ITS1) region.

In this study, we examined the identification of fungi based on the sequence homology of the internal transcribed spacer 1 (ITS1) region. A newly designed primer pair could amplify the target region of all 42 strains tested. The PCR products were sequenced and the sequence homologies were searched by BLAST. It was demonstrated that this method is a reliable identification method at the genus or species level. At present, available databases are still insufficient to identify some fungi, but with the accumulation of further data in the ITS1 database, this method will be available for the identification of fungi.

Base Sequence↗

PubMed1998

[Sequencing of Cyt b gene fragments and PCR identification of "jinqian baihuashe" (Bungarus parvus) and its adulterants].

DNAs extracted from both "Jinqian Baihuashe" (Bungarus parvus) and its adulterants and original animals of the crude snake drugs were used as templates for Cyt b gene fragment amplification. The sequence data of the fragments showed that the differences of the sequence between Bungarus parvus and its adulterants were far greater than that between intraspecific variations of Bungarus parvus. Therefore, the Cyt b gene fragment was a good molecular genetic marker for the authentication of Bungarus parvus. On the basis of the sequence data, a pair of specialized primers, BuL-1 and BuH-1 was designed for the PCR identification of Bungarus parvus. The effectiveness of the primers were examined at a series of anneal temperatures. The results showed that Bungarus parvus samples could be absolutely distinguished when the anneal temperatures were 60 degrees C-65 degrees C, whereas no incorrect or missing discrimination was found at these temperatures. The results also showed that the powder of Bungarus parvus which was mixed with powders of three other crude snake drugs may be detected by the PCR identification. This indicates that PCR identification may be a new method for examining the compositions of Chinese patent medicine.

Animals↗

PubMed2005

Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes.

Sequences of the ubiquitin-conjugating enzyme (UBC or E2) family were used as a test set to investigate issues associated with the high-throughput comparative modelling of protein structures. A semi-automatic method was initially developed with particular emphasis on producing models of a quality suitable for structural comparison. Structural and sequence features of the E2 family were used to improve the sequence alignment and the quality of the structural templates. Initially, failure to correct for subtle structural inconsistencies between templates lead to problems in the comparative analysis of the UBC electrostatic potentials. Modelling of known UBC structures using Modeller 4.0 showed that multiple templates produced, on average, no better models than the use of just one template, as judged by the root-mean-squared deviation between the comparative model and crystal structure backbones. Using four different quality-checking methods, for a given target sequence, it was not possible to distinguish the model most similar to the experimental structure. The UBC models were thus finally modelled using only the crystal structure template with the highest sequence identity to the target to be modelled, and producing only one model solution. Quality checking was used to reject models with obvious structural anomalies (e.g., bad side-chain packing). The resulting models have been used for a comparison of UBC structural features and of their electrostatic potentials. The work was extended through the development of a fully automated pipeline that identifies E2 sequences in the sequence databases, aligns and models them, and calculates the associated electrostatic potential.

Amino Acid Motifs↗

PubMed1997

Scoring hidden Markov models.

MOTIVATION: Statistical sequence comparison techniques, such as hidden Markov models and generalized profiles, calculate the probability that a sequence was generated by a given model. Log-odds 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 log-odds score should be deemed a match to the model. RESULTS: This paper analyses these two issues experimentally. Within the context of the Sequence Alignment and Modeling software suite (SAM), we consider a variety of null models and suitable thresholds. Additionally, we consider HMMer's log-odds scoring and SAM's original Z-scoring 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 hidden Markov model (HMM) performs well or best across all four discrimination experiments.

Algorithms↗

PubMed1995

Sequence analysis of frog rho-crystallin by cDNA cloning and sequencing: a member of the aldo-keto reductase family.

rho-Crystallin is a major enzyme crystallin present in the lenses of amphibian species with a blocked amino terminus. In order to facilitate the determination of the primary sequence of this taxon-specific crystallin, cDNA mixture was synthesized from the poly(A)+mRNA of bullfrog eye lenses. cDNAs encoding rho-crystallin were then amplified by polymerase chain reaction (PCR) using a new protocol of Rapid Amplification of cDNA Ends (RACE). PCR-amplified product corresponding to rho-crystallin was obtained, which was then subcloned into pUC18 vector and then transformed into E. coli strain JM109. Plasmids purified from the positive clones were prepared for nucleotide sequencing by the automatic fluorescence-based dideoxynucleotide chain-termination method. Sequencing more than 15 clones containing DNA inserts coding for rho-crystallin constructed only one unique and complete full-length reading frame of 975 base pairs covering a deduced protein sequence of 324 amino acids including the universal initiating methionine. It shows 96, 59, 46 and 37 percent sequence similarity to another rho-crystallin from European common frog, bovine prostaglandin-F synthase, human aldose reductase and human aldehyde reductase, respectively, revealing the close relationship between rho-crystallins from related amphibian species and its possible evolutionary relatedness with various aldo-keto reductases. In this study a phylogenetic tree for rho-crystallin and related enzymes is constructed based on multiple-sequence alignment program using a combination of distance matrix and approximate parsimony methods. We have thus established the remote phylogenetic relationship between rho-crystallin and some aldehyde/aldose reductases, which may provide a possible link for the recruitment of this crystallin from detoxification-related enzymes and its physiological role in maintaining a transparent and clear lens.

Alcohol Oxidoreductases↗

PubMed2002

PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.

MOTIVATION: DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers using DNA fragments that are specific to individual open reading frames (ORFs). RESULTS: PRIMEGENS first carries out a BLAST search for each target ORF against all other ORFs of the genome to quickly identify possible homologous sequences. Then it performs optimal sequence alignment between the target ORF and each of its homologous ORFs using dynamic programming. PRIMEGENS uses the sequence alignments to select gene- specific fragments, and then feeds the fragments to the Primer3 program to design primer pairs for PCR amplification. PRIMEGENS can be run from the command line on Unix/Linux platforms as a stand-alone package or it can be used from a Web interface. The program runs efficiently, and it takes a few seconds per sequence on a typical workstation. PCR primers specific to individual ORFs from Shewanella oneidensis MR-1 and Deinococcus radiodurans R1 have been designed. The PCR amplification results indicate that this method is very efficient and reliable for designing specific probes for microarray analysis.

Algorithms↗

PubMed1996

(Probably) all possible protein folds at low resolution.

For decades, a large number of investigators have been sifting the database of experimentally determined three-dimensional protein structures to discover recurring patterns of all types. Now that there are over a thousand such structures available, the natural question is whether we have seen all substantially different protein folds, and if not, how many have yet to be discovered? Answering the question can be broken down into three steps: (1) choose the range and domain for a similarity function, then (2) choose a particular similarity function, and (3) construct a corresponding protein model space that can be searched for dissimilar structures. In our analysis of the problem, we first chose to examine different conformations of the same protein, taking into account only C alpha atomic coordinates. In particular, we do not compare proteins of different chain lengths on the basis of some kind of gapped alignment. Secondly, we use a measure of conformational similarity based on rigid body superposition that emphasizes overall geometric resemblance, rather than agreement in secondary structure, for example. Third, we employed the discrete cosine transform to construct exhaustive sets of globular self-avoiding C alpha traces that were all different from each other by a given level. These sets of artificial structures were not too large to explicitly enumerate as long as the level of dissimilarity was high, and the chain flexibility was low. For chains flexible enough to match all experimental structures of 170 residue or less that are not beta-barrels, we find 128 artificial structures, of which 28 resemble nothing in the Protein Data Bank.

Amino Acid Sequence↗

PubMed2002

Comparative ab initio prediction of gene structures using pair HMMs.

We present a novel comparative method for the ab initio prediction of protein coding genes in eukaryotic genomes. The method simultaneously predicts the gene structures of two un-annotated input DNA sequences which are homologous to each other and retrieves the subsequences which are conserved between the two DNA sequences. It is capable of predicting partial, complete and multiple genes and can align pairs of genes which differ by events of exon-fusion or exon-splitting. The method employs a probabilistic pair hidden Markov model. We generate annotations using our model with two different algorithms: the Viterbi algorithm in its linear memory implementation and a new heuristic algorithm, called the stepping stone, for which both memory and time requirements scale linearly with the sequence length. We have implemented the model in a computer program called DOUBLESCAN. In this article, we introduce the method and confirm the validity of the approach on a test set of 80 pairs of orthologous DNA sequences from mouse and human. More information can be found at: http://www.sanger.ac.uk/Software/analysis/doublescan/

Algorithms↗