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At least 1,639 records · Page 91Linked to original sources
PubMed2004

BIAS: Bioinformatics Integrated Application Software.

MOTIVATION: We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system and supports standards and data-exchange protocols common to Bioinformatics. AVAILABILITY: BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/~bias/. This website also contains a paper containing a more detailed description of BIAS and a sample implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. CONTACT: hallett@mcb.mcgill.ca.

Computational Biology↗
PubMed2004

An enhanced Java graph applet interface for visualizing interactomes.

UNLABELLED: We have developed several new navigation features for a Java graph applet previously released for visualizing protein-protein interactions. This graph viewer can be used to navigate any molecular interactome dataset. We have successfully implemented this tool for exploring protein networks stored in the Bioverse interaction database. AVAILABILITY: http://bioverse.compbio.washington.edu/viewer CONTACT: ram@compbio.washington.edu.

Animals↗
PubMed2005

jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.

jPHYDIT is a Java application designed to furnish a visual and integrated environment for molecular phylogeny. The program can be used to visualize intra-strand base-pairing information in secondary and tertiary structures of ribosomal RNA (rRNA) sequences. A function for the semi-automated alignment was included to facilitate handling of the database containing a large number of multiple-aligned rRNA sequences. Integration of nucleotide sequence editing, pairwise alignment, multiple alignment and phylogenetic treeing functions provide an easy and efficient way of analyzing rRNA sequences for molecular evolution, systematics, epidemiology and ecology.

Algorithms↗
PubMed2005

Automated Microarray Image Analysis Toolbox for MATLAB.

UNLABELLED: The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source, microarray image analysis tool that allows the user to customize analyses of microarray image sets. This tool provides several methods to identify and quantify spot statistics, as well as extensive diagnostic statistics and images to evaluate data quality and array processing. The open, modular nature of AMIA provides access to implementation details and encourages modification and extension of AMIA's capabilities. AVAILABILITY: The AMIA Toolbox is freely available at http://www.pnl.gov/statistics/amia. The AMIA Toolbox requires MATLAB 6.5 (R13) (MathWorks, Inc. Natick, MA), as well as the Statistics Toolbox 4.1 and Image Processing Toolbox 4.1 for MATLAB or more recent versions. CONTACT: amanda.white@pnl.gov

Algorithms↗
PubMed2005

DEPD: a novel database for differentially expressed proteins.

SUMMARY: The Differentially Expressed Protein Database was designed to store the output of comparative proteomics studies and provides a publicly available query and analysis platform for data mining. The database contains information about more than 3000 differentially expressed proteins (DEPs) manually extracted from the published literature, including relevant biological, experimental and methodological elements. Tools for visualization and functional analysis of DEPs are provided via a user-friendly webinterface. AVAILABILITY: http://protchem.hunnu.edu.cn/depd/.

Computational Biology↗
PubMed2005

SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.

SUMMARY: SpA is a web-accessible system for the management, visualization and statistical analysis of T-cell receptor spectratype data. Users upload data from their spectratype analyzers to SpA, which saves the raw data and user-defined supplementary covariates to a secure database. The statistical engine performs several data analyses and statistical summaries. The visualization engine displays spectratype histograms in a Java applet and in an image file suitable for download. All of these results are also saved to the database and remain accessible to the user. Additional statistical tools specific to the analysis of multiple spectratypes are also available through the SpA interface. AVAILABILITY: The service is freely accessible via the web at http://www.duke.edu/~kepler/spa.html. Additional technical support and specialized statistical analysis and consultation are available by arrangement with the authors and, depending on the service requested, may be subject to fee.

Animals↗
PubMed2005

MESHI: a new library of Java classes for molecular modeling.

UNLABELLED: Adapting a modular and object-oriented approach in the design of molecular modeling packages may reduce the software development barrier between ideas and their programed applications. Towards this goal we developed MESHI, a new, strictly object-oriented, molecular modeling suite written in Java. MESHI provides a comprehensive library of extendable classes for all the essential components of molecular modeling: molecular and geometry elements, energy functions and optimization methods. AVAILABILITY: MESHI and its related documentation are freely available at http://www.cs.bgu.ac.il/~meshi; the MESHI API is available at http://www.cs.bgu.ac.il/~meshi/API CONTACT: keasar@cs.bgu.ac.il SUPPLEMENTARY INFORMATION: The Supplementary information includes (1) a detailed description of several key packages and classes, and (2) a brief presentation of results achieved by using the MESHI application--Beautify--in the CASP6 experiment.

Computer Simulation↗
PubMed2005

Design of long oligonucleotide probes for functional gene detection in a microbial community.

MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes. RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set. AVAILABILITY: http://brcapp.kribb.re.kr/HPD/

Algorithms↗
PubMed2005

MILVA: an interactive tool for the exploration of multidimensional microarray data.

MOTIVATION: Clustering techniques such as k-means and hierarchical clustering are commonly used to analyze DNA microarray derived gene expression data. However, the interactions between processes underlying the cell activity suggest that the complexity of the microarray data structure may not be fully represented with discrete clustering methods. RESULTS: A newly developed software tool called MILVA (microarray latent visualization and analysis) is presented here to investigate microarray data without separating gene expression profiles into discrete classes. The underpinning of the MILVA software is the two-dimensional topographic representation of multidimensional microarray data. On this basis, the interactive MILVA functions allow a continuous exploration of microarray data driven by the direct supervision of the biologist in detecting activity patterns of co-regulated genes. AVAILABILITY: The MILVA software is freely available. The software and the related documentation can be downloaded from http://www.ncrg.aston.ac.uk/Projects/milva. User 'surrey' as username and '3245' as password to login. The software is currently available for Windows platform only.

Cluster Analysis↗
PubMed2005

Doelan: a solution for quality control monitoring of microarray production.

SUMMARY: Doelan is an automated tool designed to monitor the quality of DNA microarray production. The software executes a series of quality control tests on hybridizations to validate batches of chips. The reports generated by Doelan should help microarray platforms aiming at quality labels, such as ISO 9001 certification. The Doelan application is written in Java and works with a plug-in system that allows everyone to add custom validation tests. AVAILABILITY: The Doelan application is distributed under the GNU General Public License at http://transcriptome.ens.fr/doelan/

Algorithms↗
PubMed2005

MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.

Catalysis↗
PubMed2005

ATID: a web-oriented database for collection of publicly available alternative translational initiation events.

SUMMARY: Alternative translational initiation is an important cellular mechanism contributing to the diversity of protein products and functions. We develop a database that provides a comprehensive collection of alternative translational initiation events. The purpose of this alternative translational initiation database (ATID) is to facilitate the systematic study of alternative translational initiation of genes. The current version of database contains 300 genes from Homo sapiens, Mus musculus and other species. Each of the genes has two or more isoforms due to alternative translational initiation. Resources in ATID, including gene information, alternative products of genes and domain structures of isoforms, are provided through a user-friendly web interface. AVAILABILITY: The ATID database is available for public use at http://bioinfo.au.tsinghua.edu.cn/atie/.

Amino Acid Sequence↗
PubMed2005

Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.

MOTIVATION: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.

Computational Biology↗
PubMed2005

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.

SUMMARY: We describe an algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length. AVAILABILITY: The software is implemented as a Java applet at http://www.mrc-bsu.cam.ac.uk/personal/thomas/phylo_comparison/comparison_page.html. It is also available on request from the authors.

Algorithms↗
PubMed2005

OligoFaktory: a visual tool for interactive oligonucleotide design.

SUMMARY: The OligoFaktory is a set of tools for the design, on an arbitrary number of target sequences, of high-quality long oligonucleotide for micro-array, of primer pair for PCR, of siRNA and more. The user-centered interface exists in two flavours: a web portal and a standalone software for Mac OS X Tiger. A unified presentation of results provides overviews with distribution charts and relative location bar graphs, as well as detailed features for each oligonucleotide. Input and output files conform to a common XML interchange file format to allow both automatic generation of input data, archiving, and post-processing of results. The design pipeline can use BLAST servers to evaluate specificity of selected oligonucleotides. AVAILABILITY: The web portal http://ueg.ulb.ac.be/oligofaktory/; the software for Macintosh: http://www.oligofaktory.org/

Algorithms↗
PubMed2005

Nexplorer: phylogeny-based exploration of sequence family data.

SUMMARY: Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics. AVAILABILITY: Web access is from http://www.molevol.org/nexplorer

Animals↗
PubMed2005

Improved spliced alignment from an information theoretic approach.

MOTIVATION: mRNA sequences and expressed sequence tags represent some of the most abundant experimental data for identifying genes and alternatively spliced products in metazoans. These transcript sequences are frequently studied by aligning them to a genomic sequence template. For existing programs, error-prone, polymorphic and cross-species data, as well as non-canonical splice sites, still present significant barriers to producing accurate, complete alignments. RESULTS: We took a novel approach to spliced alignment that meaningfully combined information from sequence similarity with that obtained from PSSM splice site models. Scoring systems were chosen to maximize their power of discrimination, and dynamic programming (DP) was employed to guarantee optimal solutions would be found. The resultant program, EXALIN, performed better than other popular tools tested under a wide range of conditions that included detection of micro-exons and human-mouse cross-species comparisons. For improved speed with only a marginal decrease in splice site prediction accuracy, EXALIN could perform limited DP guided by a result from BLASTN. AVAILABILITY: The source code, binaries, scripts, scoring matrices and splice site models for human, mouse, rice and Caenorhabditis elegans utilized in this study are posted at http://blast.wustl.edu/exalin. The software (scripts, source code and binaries) is copyrighted but free for all to use.

Algorithms↗