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At least 127 records · Page 7Linked to original sources
PubMed2002

Evaluation of internal transcribed spacer region of ribosomal DNA sequence analysis for molecular characterization of Candida albicans and Candida dubliniensis isolates from HIV-infected patients.

Molecular typing systems have been needed to study Candida colonization in HIV-infected patients, particularly for investigating virulence and fluconazole resistance. Three methods--electrophoretic karyotyping (EK), detection of restriction fragment length polymorphisms (RFLP) and randomly amplified polymorphic DNA analysis (RAPD)--have been most frequently used. In this study, comparative sequence analysis of the internal transcribed spacer (ITS) region of rDNA was evaluated for delineation of Candida isolates from 14 HIV-infected patients. EK, ITS sequence analysis, RFLP and RAPD resulted in 11, 10, 9 and 8 DNA genotypes, respectively, from 39 Candida albicans isolates. The 10 genotypes observed using ITS sequence analysis were defined by six variation sites in the sequence. Molecular typing of sequential oral isolates showed the persistence of the same genotype of C. albicans in nine patients, and genotype variation in one patient. EK and RAPD showed that another patient was co-infected by two distinct genotypes and ITS analysis identified one of the two genotypes as Candida dubliniensis. Comparative ITS sequence analysis is a quick and reproducible method that provides clear and objective results, and it also identifies C. dubliniensis. The discriminatory power of this new typing approach could be improved by concomitant analysis of other DNA polymorphic sequences.

AIDS-Related Opportunistic Infections↗
PubMed2001

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

5' Untranslated Regions↗
PubMed2005

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

Algorithms↗
PubMed2001

Sequence analysis with the Kestrel SIMD parallel processor.

Computer aided sequence analysis is a critical aspect of current biological research. Sequence information from the genome sequencing projects fills databases so quickly that humans cannot examine it all. Hence there is a heavy reliance on computer algorithms to point out the few important nuggets for human examination. Sequence search algorithms range from simple to complex, as does the representation of the biological data. Typically though, simple algorithms are used on the simplest of data representations because of the large computational demands of anything more complex. This leads to missed hits because the simple search techniques are often not sufficiently sensitive. Here we describe the implementation of several sensitive sequence analysis algorithms on the Kestrel parallel processor, a single-instruction multiple-data (SIMD) processor developed and built at UCSC. Performance of the Smith-Waterman and Hidden Markov Model algorithms, with both Viterbi and Expectation Maximization methods ranges from 6 to 20 times faster than standard computers.

Algorithms↗
PubMed2004

Analysis for free: comparing programs for sequence analysis.

Programs to import, manage and align sequences and to analyse the properties of DNA, RNA and proteins are essential for every biological laboratory. This review describes two different freeware (BioEdit and pDRAW for MS Windows) and a commercial program (Sequencher for MS Windows and Apple MacOS). Bioedit and Sequencher offer functions such as sequence alignment and editing plus reading of sequence trace files. pDRAW is a very comfortable visualisation tool with a variety of analysis functions. While Sequencher impresses with a very user-friendly interface and easy-to-use tools, BioEdit offers the largest and most customisable variety of tools. The strength of pDRAW is drawing and analysis of single sequences for priming and restriction sites and virtual cloning. It has a database function for user-specific oligonucleotides and restriction enzymes.

Base Sequence↗
PubMed2006

[Sequence analysis of ITS2 and CO1 genes of Paragonimus harinasutai].

OBJECTIVE: To identify Paragonimus harinasutai from Ninghai, Zhejiang Province, China. METHODS: Metacercariae were collected from the crabs Sinopotamon chekiangenes in Xixi village of Ninghai County for ITS2 sequence analysis, CO1 sequence analysis and endonuclease BsaHI and StuI analysis by PCR-RFLP. Results The fingerprintings of PCR-RFLP were virtually same to the isolate from Thailand (Nakorn-nayok). The ITS2 sequence with 366 bp and CO1 sequence with 390 bp of the metacercariae collected from Ninghai revealed a nucleotide identity 95.6% and 89.5% respectively to the Thai isolate. CONCLUSION: The study confirmed that Paragonimus harinasutai is present in Ninghai, China, with certain variation on molecular biology in comparison to the Thai isolate.

Animals↗
PubMed1995

Broad-range PCR amplification and DNA sequence analysis reveals variable motifs in 16S rRNA genes of Mobiluncus species.

Using DNA primers based on highly conserved regions of bacterial 16S ribosomal RNA genes, a technique was established for detection of Mobiluncus species by polymerase chain reaction (PCR) and hybridization analysis. Part of the 16S rRNA genes of Mobiluncus mulieris, Mobiluncus curtisii and uncharacterized Mobiluncus strains were analyzed by broad-range PCR amplification and direct DNA sequencing analysis. Sequence comparison of the partial 16S rRNA genes of Mobiluncus curtisii, Mobiluncus mulieris and atypical Mobiluncus strains studied indicated genus and species-specific motifs within the variable regions V3, V4 and V9 of 16S ribosomal DNAs. A Mobiluncus curtisii-specific primer, located within the variable region V3 of the 16S rRNA gene, was designed for Southern blot hybridization analysis of broad-range PCR products. Broad-range amplification combined with a M. curtisii-specific hybridization probe, Mob V3, distinguished between Mobiluncus curtisii, Mobiluncus mulieris, and atypical Mobiluncus strains.

Base Sequence↗
PubMed2000

Alfresco--a workbench for comparative genomic sequence analysis.

Comparative analysis of genomic sequences provides a powerful tool for identifying regions of potential biologic function; by comparing corresponding regions of genomes from suitable species, protein coding or regulatory regions can be identified by their homology. This requires the use of several specific types of computational analysis tools. Many programs exist for these types of analysis; not many exist for overall view/control of the results, which is necessary for large-scale genomic sequence analysis. Using Java, we have developed a new visualization tool that allows effective comparative genome sequence analysis. The program handles a pair of sequences from putatively homologous regions in different species. Results from various different existing external analysis programs, such as database searching, gene prediction, repeat masking, and alignment programs, are visualized and used to find corresponding functional sequence domains in the two sequences. The user interacts with the program through a graphic display of the genome regions, in which an independently scrollable and zoomable symbolic representation of the sequences is shown. As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of the UTY locus is presented.

Algorithms↗
PubMed1974

DNA sequence analysis: a formula to predict electrophoretic mobilities of oligonucleotides on cellulose acetate.

A simple method has recently become available for sequence analysis of large oligonucleotide fragments. Sequences are derived from the characteristic mobility shifts of the sequential partial degradation products of the oligonucleotide on two dimensional homochromatography. We have now developed an empirical formula for predicting the relative mobilities of each of the partial products in the first dimension (electrophoresis on cellulose acetate gel). The formula allows a more precise interpretation of the sequence of the oligonucleotide. It eliminates the ambiguities present in the method previously reported for sequence analysis by simple inspection of the mobility shifts. In order to amplify the mobility shifts so that they may be more easily and accurately measured, methods have been developed for preparing and fractionating the oligonucleotides on 40 x 40 cm DEAE-cellulose plates. Both improvements have proven valuable for direct sequence analysis by mapping.

Algorithms↗
PubMed2000

DNASTAR's Lasergene sequence analysis software.

Lasergene's eight modules provide tools that enable users to accomplish each step of sequence analysis, from trimming and assembly of sequence data, to gene discovery, annotation, gene product analysis, sequence similarity searches, sequence alignment, phylogenetic analysis, oligonucleotide primer design, cloning strategies, and publication of the results. The Lasergene software suite provides the functions and customization tools needed so that users can perform analyses the software writers never imagined.

Base Sequence↗
PubMed2002

Elaboration of some sequence analysis strategies: examples and guidelines for level of confidence.

Although not the only way to approach the interpretation of Rorschach test data, the Comprehensive System (Exner, 1991) search strategy is the most systematized and empirically informed to date. Within that search strategy, a role for sequence analysis remains (Weiner, 1998). Sequence analysis adds a specificity of nuance useful in bringing personal meaning to, answering more difficult test questions about, or explaining apparent incongruities in the data. In this article, I elaborate a few aspects of some particular sequence analysis strategies as a way of supplementing Weiner's (1998) description. I discuss and expand the following ideas: (a) conjoint (configurational) examination of individual responses, (b) specifics about patient concerns, (c) specifics about response deterioration and their treatment implications, (d) specifics about response recovery and their treatment implications, (e) contribution of attitude toward the response, (f) minisequence and configurational analysis strategies for particular test questions, and (g) guidelines for establishing level of confidence in sequence analysis inferences.

Guidelines as Topic↗
PubMed1988

Statistical geometry in sequence space: a method of quantitative comparative sequence analysis.

A statistical method of comparative sequence analysis that combines horizontal and vertical correlations among aligned sequences is introduced. It is based on the analysis mainly of quartet combinations of sequences considered as geometric configurations in sequence space. Numerical invariants related to relative internal segment lengths are assigned to each such configuration and statistical averages of these invariants are established. They are used for internal calibration of the topology of divergence and for quantitative determination of the noise level. Comparison of computer simulations with experimental data reveals the high sensitivity of assignment of basic topologies even if much randomized. In addition, these procedures are checked by vertical analysis of the aligned sequences to allow the study of divergences with positionally varying substitution probabilities.

Base Sequence↗
PubMed1995

DNA Strider. An inexpensive sequence analysis package for the Macintosh.

DNA Strider is a user-friendly Macintosh program designed for analysis of molecular sequence data. The program shows great versatility in choice of genetic codes, restriction enzymes, algorithms for hydropathy plots, and interconversions between types of sequence data. It is very straightforward and interacts well with other sequence and phylogenetic analysis packages, importing and exporting data easily. The graphic outputs can be used directly for manuscript-quality figures, or exported to more sophisticated text or graphic programs.

Amino Acid Sequence↗
PubMed1992

Characterization of the gill symbiont of Thyasira flexuosa (Thyasiridae: Bivalvia) by use of polymerase chain reaction and 16S rRNA sequence analysis.

Comparative molecular sequence (16S rRNA) analysis methods were used to identify and characterize the symbionts of Thyasira flexuosa independently of pure culture techniques and to compare these symbionts with the previously reported putative symbiont isolate, Thiobacillus thyasiris TG-2 (A. P. Wood and D. P. Kelly, Arch. Microbiol. 152:160-166, 1989). Polymerase chain reaction amplification using 16S rRNA primers specific for eubacteria was used to amplify a single unique sequence from the gill tissue of T. flexuosa. This sequence is phylogenetically most closely related to the 16S rRNA genes of known symbionts of lucinid clams and is distinct from those determined for strain TG-2 and other known bacteria. Strain TG-2 most closely resembles a free-living, chemolithoautotrophic bacterium known to be associated with the surfaces of thiotrophic bivalve shells, suggesting that this strain is a contaminant and not the authentic intracellular symbiont of T. flexuosa.

Animals↗
PubMed2004

Corynebacterium species isolated from bone and joint infections identified by 16S rRNA gene sequence analysis.

By the use of 16S rRNA gene sequence analysis we identified 28 of 31 Corynebacterium spp. isolated from bone and joint infections, including species never before isolated in such infections. Phenotypic analysis led to the correct identification of 8 of 31. 16S rRNA gene sequence analysis appears to be a good technique for identification of clinical strains of Corynebacterium spp.

Adult↗
PubMed1986

Mitotic recombination in germ cells generated two major histocompatibility complex mutant genes shown to be identical by RNA sequence analysis: Kbm9 and Kbm6.

RNA sequencing represents a major procedural simplification for nucleotide sequence analysis of a transcribed gene. Using newly adapted mRNA and cDNA sequencing procedures, we have sequenced 855 nucleotides of Kbm9 mRNA, corresponding to the codons for the aminoterminal 285 amino acids. The inferred DNA sequence of the Kbm9 gene differs from the parental Kb sequence by single nucleotide alterations in each of codons 116 and 121, resulting in Tyr----Phe and Cys----Arg substitutions, respectively. The Kbm9 sequence is identical to that of another independently arising MHC mutant gene, Kbm6. As both the Kbm9 and Kbm6 genes were generated by recombination between the Kb and Q4 genes, our data indicate that the identical genetic interactions have occurred at least twice. The relatively large extent of identity between Q4 and Kb may be responsible for frequent recombination between the two genes. The parents of the original bm9 mutant mice had five identical mutant offspring, which can be explained by mitotic recombination in the germ cells, producing gonadal mosaicism in the C57BL/6 mother. Thus, mitotic recombination, and not meiotic recombination, appears to be responsible for the formation of at least some of the Kb mutants. Such a mechanism probably plays a major role in the generation of diversity in the major histocompatibility complex.

Animals↗