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Results for “alignment chaining method”

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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↗

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↗

PubMed1981

Studies of chromophores in model membranes by polarized light-absorption spectroscopy. The orientation and binding of tetracaine and procaine.

A method for studying the orientation and binding of chromophores in macroscopically aligned membranes by polarized light absorption spectroscopy is described. Here tetracaine and procaine solubilized in a lamellar phase of octanoyl-1-glyceride (monooctanoin) and water have been investigated. Tetracaine is found to be located in the lipid region with a preferential orientation of the molecular long axis parallel to the hydrocarbon chains. The orientation of procaine, mainly residing in the water region, is very small.

Binding Sites↗

PubMed1988

Trypanothione reductase of Trypanosoma congolense: gene isolation, primary sequence determination, and comparison to glutathione reductase.

The gene encoding trypanothione reductase, the redox disulfide-containing flavoenzyme that is unique to the parasitic trypanosomatids (Shames et al., 1986), has been isolated from the cattle pathogen Trypanosoma congolense. Library screening was carried out with inosine-containing oligonucleotide probes encoding sequences determined from two active site peptides isolated from the purified Crithidia fasciculata enzyme. The nucleotide sequence of the gene was determined according to the dideoxy chain termination method of Sanger. The structural gene is 1476 nucleotides long and encodes 492 amino acids. We have identified the active site peptide containing the redox-active disulfide, a peptide corresponding to the histidine-467 region of human erythrocyte glutathione reductase, as well as the flavin binding domain that is highly conserved in all disulfide-containing flavoprotein reductase enzymes. Alignment of five tryptic peptides (80 residues) isolated from the C. fasciculata trypanothione reductase with the primary sequence of the T. congolense enzyme showed 88% homology with 76% identity. Additionally, a sequence comparison of the glutathione reductase from Escherichia coli or human erythrocytes to T. congolense trypanothione reductase reveals greater than 50% homology. A search for the amino acid residues in the primary sequence of trypanothione reductase functionally active in binding/catalysis in human erythrocyte glutathione reductase shows that only the two arginine residues (Arg-37 and Arg-347), shown by X-ray crystallographic data to hydrogen bond to the GS1 glutathione glycyl carboxylate, are absent.

Amino Acid Sequence↗

PubMed1979

[Hemoglobins, XXV. Hemoglobin (erythrocruorin) CTT III from Chironomus thummi thummi (Diptera). Primary structure and relationship to other heme proteins (author's transl)].

The amino acid sequence analysis of hemoglobin (erythrocruorin) CTT III from Chironomus thummi th. (Diptera) has been checked with automatic methods and completed. The protein chain consists of 136 amino acids and contains a neutral exchange isoleucine/threonine in position 57. The molecular weight of the heme protein (Thr) is 15400. The primary structure gives the chemical basis for the refinement of the X-ray structure and the understanding of the mechanism of the Bohr effect in this monomeric hemoglobin. A homologous alignment to vertebrate globins is reported. The resulting data for the phylogeny of proto-and deuterostomian animals and the function of this hemoglobin are discussed.

Amino Acid Sequence↗

PubMed1992

Isolation and sequence analysis of the small subunit ribosomal RNA gene from the euryhaline yeast Debaryomyces hansenii.

The small subunit ribosomal RNA gene (SSU rDNA) from the euryhaline yeast Debaryomyces hansenii has been isolated and sequenced. After appropriate alignment of this sequence with SSU rDNA sequences from 30 other taxa, phylogenetic reconstruction using distance matrix and maximum parsimony methods indicates that D. hansenii is most closely affiliated with Candida albicans, and occurs in the cluster of the yeasts Saccharomyces cerevisiae, Torulaspora delbruekii, Candida glabrata, and Kluyveromyces lactis. It appears that the capacity to tolerate high salt is independent of phylogenetic affiliations based on SSU rDNA analyses.

Base Sequence↗

PubMed2003

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

This article presents an overview of the SAM-T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM-T02 server is an automatic method that uses two-track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two-track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment-packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold-recognition alignments from the SAM-T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139.

Algorithms↗

PubMed2004

A neural network method for prediction of beta-turn types in proteins using evolutionary information.

MOTIVATION: The prediction of beta-turns is an important element of protein secondary structure prediction. Recently, a highly accurate neural network based method Betatpred2 has been developed for predicting beta-turns in proteins using position-specific scoring matrices (PSSM) generated by PSI-BLAST and secondary structure information predicted by PSIPRED. However, the major limitation of Betatpred2 is that it predicts only beta-turn and non-beta-turn residues and does not provide any information of different beta-turn types. Thus, there is a need to predict beta-turn types using an approach based on multiple sequence alignment, which will be useful in overall tertiary structure prediction. RESULTS: In the present work, a method has been developed for the prediction of beta-turn types I, II, IV and VIII. For each turn type, two consecutive feed-forward back-propagation networks with a single hidden layer have been used where the first sequence-to-structure network has been trained on single sequences as well as on PSI-BLAST PSSM. The output from the first network along with PSIPRED predicted secondary structure has been used as input for the second-level structure-to-structure network. The networks have been trained and tested on a non-homologous dataset of 426 proteins chains by 7-fold cross-validation. It has been observed that the prediction performance for each turn type is improved significantly by using multiple sequence alignment. The performance has been further improved by using a second level structure-to-structure network and PSIPRED predicted secondary structure information. It has been observed that Type I and II beta-turns have better prediction performance than Type IV and VIII beta-turns. The final network yields an overall accuracy of 74.5, 93.5, 67.9 and 96.5% with MCC values of 0.29, 0.29, 0.23 and 0.02 for Type I, II, IV and VIII beta-turns, respectively, and is better than random prediction. AVAILABILITY: A web server for prediction of beta-turn types I, II, IV and VIII based on above approach is available at http://www.imtech.res.in/raghava/betaturns/ and http://bioinformatics.uams.edu/mirror/betaturns/ (mirror site).

Algorithms↗

PubMed2003

Cyclospora cayetanensis: a review of an emerging parasitic coccidian.

Cyclospora cayetanensis is a sporulating parasitic protozoan that infects the upper small intestinal tract. It has been identified as both a food and waterborne pathogen endemic in many developing countries. It is an important agent of Traveller's Diarrohea in developed countries and was responsible for numerous foodborne outbreaks in the United States and Canada in the late 1990s. Like Cryptosporidium, infection has been associated with a variety of sequelae such as Guillain-Barré syndrome, reactive arthritis syndrome (formally Reiter syndrome) and acalculous cholecystitis. There has been much debate as to where to place C. cayetanensis taxonomically due to its homology with Eimeria species. To date, the only genomic DNA sequences available are the ribosomal DNA of C. cayetanensis and three other species; within these a high degree of homology has been observed. This homology and the lack of sequence data from other Cyclospora species have hindered identification methods.

Animals↗

PubMed2000

The role of pattern databases in sequence analysis.

In the wake of the numerous now-fruitful genome projects, we are entering an era rich in biological data. The field of bioinformatics is poised to exploit this information in increasingly powerful ways, but the abundance and growing complexity both of the data and of the tools and resources required to analyse them are threatening to overwhelm us. Databases and their search tools are now an essential part of the research environment. However, the rate of sequence generation and the haphazard proliferation of databases have made it difficult to keep pace with developments. In an age of information overload, researchers want rapid, easy-to-use, reliable tools for functional characterisation of newly determined sequences. But what are those tools? How do we access them? Which should we use? This review focuses on a particular type of database that is increasingly used in the task of routine sequence analysis--the so-called pattern database. The paper aims to provide an overview of the current status of pattern databases in common use, outlining the methods behind them and giving pointers on their diagnostic strengths and weaknesses.

Amino Acid Motifs↗

PubMed1998

The rrs (16S)-rrl (23S) ribosomal intergenic spacer region as a target for the detection of Haemophilus ducreyi by a heminested-PCR assay.

The intergenic spacer region between the rrs and rrl ribosomal RNA genes of Haemophilus ducreyi was analysed and the DNA sequence was used for the selection of specific PCR primers. A highly sensitive and specific heminested-PCR assay for the identification of H. ducreyi was developed. The assay showed a sensitivity of 96% on genital ulcer specimens from patients with clinically diagnosed chancroid, compared with a sensitivity of 56% for culture methods. These results indicate that this PCR assay has the potential to become an accurate and easy reference method for the detection of H. ducreyi.

Base Sequence↗