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At least 1,765 records · Page 98Linked to original sources
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

ClaNC: point-and-click software for classifying microarrays to nearest centroids.

SUMMARY: ClaNC (classification to nearest centroids) is a simple and an accurate method for classifying microarrays. This document introduces a point-and-click interface to the ClaNC methodology. The software is available as an R package. AVAILABILITY: ClaNC is freely available from http://students.washington.edu/adabney/clanc

Algorithms↗
PubMed2005

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

Computer Graphics↗
PubMed2005

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms.

MOTIVATION: Periodic patterns in time series resulting from biological experiments are of great interest. The commonly used Fast Fourier Transform (FFT) algorithm is applicable only when data are evenly spaced and when no values are missing, which is not always the case in high-throughput measurements. The choice of statistic to evaluate the significance of the periodic patterns for unevenly spaced gene expression time series has not been well substantiated. METHODS: The Lomb-Scargle periodogram approach is used to search time series of gene expression to quantify the periodic behavior of every gene represented on the DNA array. The Lomb-Scargle periodogram analysis provides a direct method to treat missing values and unevenly spaced time points. We propose the combination of a Lomb-Scargle test statistic for periodicity and a multiple hypothesis testing procedure with controlled false discovery rate to detect significant periodic gene expression patterns. RESULTS: We analyzed the Plasmodium falciparum gene expression dataset. In the Quality Control Dataset of 5080 expression patterns, we found 4112 periodic probes. In addition, we identified 243 probes with periodic expression in the Complete Dataset, which could not be examined in the original study by the FFT analysis due to an excessive number of missing values. While most periodic genes had a period of 48 h, some had a period close to 24 h. Our approach should be applicable for detection and quantification of periodic patterns in any unevenly spaced gene expression time-series data.

Algorithms↗
PubMed2005

Multiple Alignment of protein structures and sequences for VMD.

Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the aligned structures and performing a variety of evolutionary and bioinformatic tasks, including the construction of structure-based phylogenetic trees and minimal basis sets of structures that best represent the topology of the phylogenetic tree. It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois.

Amino Acid Sequence↗
PubMed2005

RNAshapes: an integrated RNA analysis package based on abstract shapes.

We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.

Algorithms↗
PubMed2006

OPM: orientations of proteins in membranes database.

SUMMARY: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading. AVAILABILITY: http://opm.phar.umich.edu.

Computer Graphics↗
PubMed2006

A multi-step approach to time series analysis and gene expression clustering.

MOTIVATION: The huge growth in gene expression data calls for the implementation of automatic tools for data processing and interpretation. RESULTS: We present a new and comprehensive machine learning data mining framework consisting in a non-linear PCA neural network for feature extraction, and probabilistic principal surfaces combined with an agglomerative approach based on Negentropy aimed at clustering gene microarray data. The method, which provides a user-friendly visualization interface, can work on noisy data with missing points and represents an automatic procedure to get, with no a priori assumptions, the number of clusters present in the data. Cell-cycle dataset and a detailed analysis confirm the biological nature of the most significant clusters. AVAILABILITY: The software described here is a subpackage part of the ASTRONEURAL package and is available upon request from the corresponding author. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Artificial Intelligence↗
PubMed2006

Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.

MOTIVATION: Algorithmic and modeling advances in the area of protein-protein interaction (PPI) network analysis could contribute to the understanding of biological processes. Local structure of networks can be measured by the frequency distribution of graphlets, small connected non-isomorphic induced subgraphs. This measure of local structure has been used to show that high-confidence PPI networks have local structure of geometric random graphs. Finding graphlets exhaustively in a large network is computationally intensive. More complete PPI networks, as well as PPI networks of higher organisms, will thus require efficient heuristic approaches. RESULTS: We propose two efficient and scalable heuristics for finding graphlets in high-confidence PPI networks. We show that both PPI and their model geometric random networks, have defined boundaries that are sparser than the 'inner parts' of the networks. In addition, these networks exhibit 'uniformity' of local structure inside the networks. Our first heuristic exploits these two structural properties of PPI and geometric random networks to find good estimates of graphlet frequency distributions in these networks up to 690 times faster than the exhaustive searches. Our second heuristic is a variant of a more standard sampling technique and it produces accurate approximate results up to 377 times faster than the exhaustive searches. We indicate how the combination of these approaches may result in an even better heuristic. AVAILABILITY: Supplementary information is available at http://www.cs.toronto.edu/~natasha/BIOINF-2005-0946/Supplementary.pdf. Software implementing the algorithms is available at http://www.cs.toronto.edu/~natasha/BIOINF-2005-0946/estimate_grap-hlets.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed2006

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks.

SUMMARY: WebCell is a web-based environment for managing quantitative and qualitative information on cellular networks and for interactively exploring their steady-state and dynamic behaviors in response to systemic perturbations. It is designed as a user-friendly web interface, allowing users to efficiently construct, visualize, analyze and store reaction network models, thereby facilitating kinetic modeling and in silico simulation of biological systems of interest. A collected model library is also available to provide comprehensive implications for cellular dynamics of the published models.

Cell Physiological Phenomena↗
PubMed2006

Prediction of viable circular permutants using a graph theoretic approach.

MOTIVATION: In recent years graph-theoretic descriptions have been applied to aid the analysis of a number of complex biological systems. However, such an approach has only just begun to be applied to examine protein structures and the network of interactions between residues with promising results. Here we examine whether a graph measure known as closeness is capable of predicting regions where a protein can be split to form a viable circular permutant. Circular permutants are a powerful experimental tool to probe folding mechanisms and more recently have been used to design split enzyme reporter proteins. RESULTS: We test our method on an extensive set of experiments carried out on dihydrofolate reductase in which circular permutants were constructed for every amino acid position in the sequence, together with partial data from studies on other proteins. Results show that closeness is capable of correctly identifying significantly more residues which are suitable for circular permutation than solvent accessibility. This has potential implications for the design of successful split enzymes having particular importance for the development of protein-protein interaction screening methods and offers new perspectives on protein folding. More generally, the method illustrates the success with which graph-theoretic measures encapsulate the variety of long and short range interactions between residues during the folding process.

Binding Sites↗
PubMed2006

TopoICE-R: 3D visualization modeling the topology of DNA recombination.

UNLABELLED: TopoICE-R is a three-dimensional visualization and manipulation software for solving 2-string tangle equations and can be used to model the topology of DNA bound by proteins such as recombinases and topoisomerases. AVAILABILITY: This software, manual and example files are available at www.knotplot.com/download for Linux, Windows and Mac.

Algorithms↗
PubMed2006

JCell--a Java-based framework for inferring regulatory networks from time series data.

MOTIVATION: JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. AVAILABILITY: The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

Algorithms↗
PubMed2006

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

UNLABELLED: THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. AVAILABILITY: ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

Algorithms↗
PubMed2006

MAGOS: multiple alignment and modelling server.

UNLABELLED: MAGOS is a web server allowing automated protein modelling coupled to the creation of a hierarchical and annotated multiple alignment of complete sequences. MAGOS is designed for an interactive approach of structural information within the framework of the evolutionary relevance of mined and predicted sequence information. AVAILABILITY: The web server is freely available at http://pig-pbil.ibcp.fr/magos.

Algorithms↗
PubMed2006

VISTAL--a new 2D visualization tool of protein 3D structural alignments.

UNLABELLED: We offer a tool, denoted VISTAL, for two-dimensional visualization of protein structural alignments. VISTAL describes aligned structures as a series of matched secondary structure elements, colored according to the three-dimensional distance of their Calpha atoms. AVAILABILITY: VISTAL can be downloaded from http://trantor.bioc.columbia.edu/~kolodny/software.html.

Algorithms↗
PubMed2006

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.

MOTIVATION: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. Versatile software tools for interactively displaying and analyzing these networks are therefore very much in demand. The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by the scientific community. RESULTS: We present GenePro, a plugin to Cytoscape featuring a set of versatile tools that greatly facilitates the visualization and analysis of protein networks derived from high-throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules. AVAILABILITY: The GenePro plugin is available at the website http://genepro.ccb.sickkids.ca.

Algorithms↗