Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Biological sequence analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 73 records · Page 4Linked to original sources
PubMed1994

HIV type 1 variation in World Health Organization-sponsored vaccine evaluation sites: genetic screening, sequence analysis, and preliminary biological characterization of selected viral strains. WHO Network for HIV Isolation and Characterization.

A laboratory network has been established by the World Health Organization (WHO) to systematically isolate and characterize HIV strains from different parts of the world, and to obtain information and reagents that would facilitate HIV vaccine development. Sixty-three HIV-1 isolates obtained from 224 specimens collected during 1992-1993 in Brazil, Rwanda, Thailand, and Uganda were characterized in this initial study. Virus strains were first genetically subtyped using three different screening methodologies: PCR-gag fingerprinting, RNase A mismatch, and heteroduplex mobility assay (HMA). In addition, selected viruses were sequenced in V3 (52 strains), C2-V3 (42 strains), gp120 (15 strains), and/or gp160 (8 strains) regions of their envelope genes. These studies identified viruses belonging to different sequence subtypes in the four countries: 16 subtype B and 1 subtype C strains in Brazil, 13 subtype A strains in Rwanda, 15 subtype E and 2 subtype B strains in Thailand, and 3 subtype A and 13 subtype D strains in Uganda. Comparison of sequence data with results from the genetic screening efforts identified the HMA as a rapid and reliable method for sequence subtype determinations. The majority of strains were collected from persons documented to have recently seroconverted to HIV-1 positivity, and most strains were found to have slow replication and low cytopathic characteristics and to be non-syncytium-inducing (slow/low-NSI phenotypes) in vitro, which, in many cases, correlated with the corresponding genotype and charge of the V3 loop amino acid sequences. This collection of HIV strains is presently being characterized immunologically and serologically, including neutralization assays, to define whether there are immunological correlates of the sequence subtypes. Identification of potential immunotypes would be of considerable importance for the further development of HIV vaccines.

AIDS Vaccines↗
PubMed2005

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

BACKGROUND: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. RESULTS: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. CONCLUSION: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454

Algorithms↗
PubMed1980

Purification of somatomedin-C from human plasma: chemical and biological properties, partial sequence analysis, and relationship to other somatomedins.

Somatomedin-C (SM-C) was purified from Cohn fraction IV of human plasma by a series of steps which included cation-exchange chromatography, gel filtration, isoelectric focusing, and reverse-phase high-pressure liquid chromatography. The peptide isolated contained 10,142 units/mg, as judged by a radioimmunoassay, representing a 780,000-fold purification from native plasma. The isolated peptide was basic (pI 8.1-8.5) and was judged to be no less than 90% pure. The best fit for integral amino acids was obtained with 78 residues. Limited sequence data were obtained on the N terminus and on five fragments obtained by tryptic digestion after blocking the lysine residues. Three of these fragments and the N terminus could be aligned with portions of insulin-like growth factor I (IGF-I). Of the 25 residues so aligned, 22 were identical with IGF-I. In addition, two tryptic fragments were obtained which are not present in the sequence of IGF-I. SM-C and IGF-I produced identical curves of displacement in radioimmunoassay and radioreceptor assays for SM-C and in an insulin radioreceptor assay. The potencies of SM-C and IGF-I in these assays differed significantly from IGF-II, somatomedin-A, and several preparations of multiplication stimulating activity. At a concentration of 1 ng/mL, SM-C stimulated the progression of Balb/c 3T3 cells into DNA synthesis and when injected in vivo restored mitosis in lens epithelium of hypophysectomized frogs.

Amino Acid Sequence↗
PubMed1988

Molecular biological analysis of sequence-specific DNA recognition and cleavage by metallobleomycins.

The DNase I footprinting analysis shows binding sites of approximately two or three base pairs, in particular 5'-XGC sequences, for the green-colored Co(III) and fully oxidized Fe(III) complexes of bleomycin (BLM). In contrast to covalent attachment of guanine N-7 with aflatoxin B1 or dimethyl sulfate, the modification of guanine 2-amino group with anthramycin remarkably inhibits the DNA cleavages at 5'-GC and 5'-GT sites by the iron and cobalt complex systems of BLM. The present results strongly indicate that metallobleomycin binds in minor groove of B-DNA and that the 2-amino group of guanine adjacent to 5'-side of the cleaved pyrimidine base is one key element of specific 5'-GC or 5'-GT recognition by metallobleomycin. On the basis of these experimental data, possible binding mode of metallobleomycin in B-DNA helix has been proposed by computer-constructed model building.

Base Sequence↗
PubMed2001

Functional and structural genomics using PEDANT.

MOTIVATION: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it. RESULTS: The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual assignment of gene products to a number of functional and structural categories, (iv) extensive hyperlinked protein reports, and (v) advanced DNA and protein viewers. The system is easily extensible and allows to include custom methods, databases, and categories with minimal or no programming effort. PEDANT is actively used as a collaborative environment to support several on-going genome sequencing projects. The main purpose of the PEDANT genome database is to quickly disseminate well-organized information on completely sequenced and unfinished genomes. It currently includes 80 genomic sequences and in many cases serves as the only source of exhaustive information on a given genome. The database also acts as a vehicle for a number of research projects in bioinformatics. Using SQL queries, it is possible to correlate a large variety of pre-computed properties of gene products encoded in complete genomes with each other and compare them with data sets of special scientific interest. In particular, the availability of structural predictions for over 300 000 genomic proteins makes PEDANT the most extensive structural genomics resource available on the web.

Arabidopsis↗
PubMed2003

Wavelets in bioinformatics and computational biology: state of art and perspectives.

MOTIVATION: At a recent meeting, the wavelet transform was depicted as a small child kicking back at its father, the Fourier transform. Wavelets are more efficient and faster than Fourier methods in capturing the essence of data. Nowadays there is a growing interest in using wavelets in the analysis of biological sequences and molecular biology-related signals. RESULTS: This review is intended to summarize the potential of state of the art wavelets, and in particular wavelet statistical methodology, in different areas of molecular biology: genome sequence, protein structure and microarray data analysis. I conclude by discussing the use of wavelets in modeling biological structures.

Algorithms↗
PubMed2006

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein-structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at www.migenas.org (click 'Start Toolkit').

Animals↗
PubMed1994

Linguistic approaches to the analysis of sequence information.

Biological macromolecules have many features that resemble modern languages. Thus, linguistic approaches to the analysis of sequence information are becoming powerful tools for deciphering genetic texts. The methodologies used, to date, to determine the global parameters of the genetic language and meaningful patterns within it are described.

Algorithms↗
PubMed2004

BLMT: statistical sequence analysis using N-grams.

UNLABELLED: Statistical analysis of amino acid and nucleotide sequences, especially sequence alignment, is one of the most commonly performed tasks in modern molecular biology. However, for many tasks in bioinformatics, the requirement for the features in an alignment to be consecutive is restrictive and "n-grams" (aka k-tuples) have been used as features instead. N-grams are usually short nucleotide or amino acid sequences of length n, but the unit for a gram may be chosen arbitrarily. The n-gram concept is borrowed from language technologies where n-grams of words form the fundamental units in statistical language models. Despite the demonstrated utility of n-gram statistics for the biology domain, there is currently no publicly accessible generic tool for the efficient calculation of such statistics. Most sequence analysis tools will disregard matches because of the lack of statistical significance in finding short sequences. This article presents the integrated Biological Language Modeling Toolkit (BLMT) that allows efficient calculation of n-gram statistics for arbitrary sequence datasets. AVAILABILITY: BLMT can be downloaded from http://www.cs.cmu.edu/~blmt/source and installed for standalone use on any Unix platform or Unix shell emulation such as Cygwin on the Windows platform. Specific tools and usage details are described in a "readme" file. The n-gram computations carried out by the BLMT are part of a broader set of tools borrowed from language technologies and modified for statistical analysis of biological sequences; these are available at http://flan.blm.cs.cmu.edu/.

Algorithms↗
PubMed1996

Characterization of human papillomavirus type 57b: transforming activity and comparative sequence analysis as probes for biological determinants associated with high-risk oncogenic viruses.

The association of human papillomavirus type 57 (HPV-57) with premalignant and malignant tumors of the nasal cavity was previously reported (Wu et al., Lancet 341, 522, 1993). We determined the complete nucleotide sequence of HPV-57b (GenBank 37537), which was molecularly cloned from a benign fungiform papilloma, and compared it with other HPV types and HPV-57a, which was cloned from an inverted papilloma of the maxillary sinus by de Villiers et al. (Virology 171, 248. 1989). Comparative and phylogenetic analysis of amino acid sequences of the HPV-57b oncogenes E5, E6, and E7 were performed with HPV-6, 11, 16, and 18. Phylogenetic trees using the Jotun-Hein algorithm indicated a closer relationship of HPV-57b E5 and E7 with corresponding genes of HPV-18. Signature pattern analysis of these two oncogenes was also in agreement with a closer relatedness to HPV-16 and 18 oncogenes, which are associated with a high risk for malignant progression. Compared with 7861 bp of HPV-57a, HPV-57b had 7868 bp as well as differences in the restriction enzyme sites and the open reading frames, including at least five additional ones. To investigate the oncogenic potential of HPV-57b, NIH 3T3 and REF52 cells were cotransfected with two plasmids: pKP54. HPV-57b, which contains the HPV-57b genome, and pMT.neo.1, which confers resistance to G418. After selection in culture medium containing G418, 58% of the G418r NIH 3T3 colonies and 47% of the G418r REF52 colonies exhibited morphological transformation. These results indicate that the transcriptional regulatory elements and the oncoproteins of HPV-57b are active in vitro to induce cellular transformation, as are other high-risk HPV types.

3T3 Cells↗
PubMed2003

Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.

Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. In addition to web-based output, Theatre can produce publication quality colour hardcopies showing predicted features in aligned genomic sequences. A case study using the p53 promoter region of four mammalian species and two fish species is described. Unlike the mammalian sequences the promoter regions in fish have not been previously predicted or characterized and we report the differences in the p53 promoter region of four mammals and that predicted for two fish species. Theatre can be accessed at http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/.

Animals↗
PubMed2002

Analysis of information content for biological sequences.

Decomposing a biological sequence into modular domains is a basic prerequisite to identify functional units in biological molecules. The commonly used segmentation procedures usually have two steps. First, collect and align a set of sequences that are homologous to the target sequence. Then, parse this multiple alignment into several blocks and identify the functionally important ones by using a semi-automatic method, which combines manual analysis and expert knowledge. In this paper, we present a novel exploratory approach to parsing and analyzing such kinds of multiple alignments. It is based on a type of analysis-of-variance (ANOVA) decomposition of the sequence information content. Unlike the traditional change-point method, this approach takes into account not only the composition biases but also the overdispersion effects among the blocks. The new approach is tested on the families of ribosomal proteins and has a promising performance. It is shown that the new approach provides a better way for judging some important residues in these proteins. This allows one to find some subsets of residues, which are critical to these proteins.

Algorithms↗
PubMed1996

[Beta-heterochromatin in Drosophila: molecular organization and function. Molecular biological analysis of a MAR/SAR DNA sequence in centromere heterochromatin of Drosophila melanogaster].

A molecular biological characteristic of a DNA fragment delta 20p1.4, which is a moderately repetitive sequence of the Drosophila melanogaster genome, is presented. The fragment is present in about 120 copies per haploid genome. The main pool of the delta 20p1.4 homologous DNA can be isolated, along with the nuclear matrix DNA, and consists of Hind III-EcoR I monomers 1.4-1.6 kb in length. The monomers may occur in the genome as both single copies and tandem clusters forming chromosomes fragments up to 6-10 kb in length. The region of the delta 20p1.4 fragment between nucleotides 350 and 905 polymerizes with purified lamin from D. melanogaster. The sites of the fragment that had physical contact with lamin in vitro were determined using an Exo III protection. It was demonstrated that ATATTT, A, and T boxes located in four nonperfect tandem repeats were involved in the contact, both DNA strains reacting with lamin.

Animals↗
PubMed1997

Analysis of sequence requirements for biological activity of cyanovirin-N, a potent HIV (human immunodeficiency virus)-inactivating protein.

Site-directed mutagenesis of DNA constructs coding for the novel, HIV-inactivating proteins cyanovirin-N (CV-N) and FLAG-cyanovirin-N (F-CV-N) was performed using mutagenic oligonucleotide primers in the polymerase chain reaction or by a restriction site elimination maneuver. The mutant constructs were expressed in Escherichia coli and the recombinant protein products were tested for binding to the HIV surface envelope glycoprotein gp 120 and for antiviral activity against infectious HIV. Results showed an overall very high correlation (r2 > 0.9) between the relative gp120 binding affinities and the anti-HIV activities of CV-N, F-CV-N, and the various mutants. An outlier, however, was a mutant which lacked one of the internal disulfide linkages normally present in CV-N and which showed modest gp120 binding but no antiviral activity against HIV. These findings are consistent with the view that gp120 binding is a necessary but not sufficient requirement for the HIV-inactivating activity of CV-N and related proteins; the sequence specificities for gp120 binding and anti-HIV activity are not identical.

Amino Acid Sequence↗
PubMed2003

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes.

Dramatic progress in deciphering the regulatory controls in Saccharomyces cerevisiae has been enabled by the fusion of high-throughput genomics technologies with advanced sequence analysis algorithms. Sets of genes likely to function together and with similar expression profiles have been identified in diverse studies. By fusing an advanced pattern recognition algorithm for identification of transcription factor binding sites with a new method for the quantitative comparison of binding properties of transcription factors, we provide an integrated means to move from expression data to biological insights. The Yeast Regulatory Sequence Analysis system, YRSA, combines standard functions with a novel pattern characterization procedure in an intuitive interface designed for use by a broad range of scientists. The features of the system include automated retrieval of user-defined promoter sequences, binding site discovery by pattern recognition, graphical displays of the observed pattern and positions of similar sequences in the specified genes, and comparison of the new pattern against a collection of binding patterns for characterized transcription factors. The comprehensive YRSA system was used to study the regulatory mechanisms of yeast regulons. Analysis of the regulatory controls of a battery of genes induced by DNA damaging agents supports a putative mediating role for the cell-cycle checkpoint regulatory element MCB. YRSA is available at http://yrsa.cgb.ki.se. [YRSA: ancient Scandinavian name meaning old she-bear (Latin Ursus arctos = brown bear/grizzly).]

Algorithms↗