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At least 1,693 records · Page 94Linked to original sources

PubMed2006

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

MOTIVATION: Tandem mass spectrometry (MS/MS) identifies protein sequences using database search engines, at the core of which is a score that measures the similarity between peptide MS/MS spectra and a protein sequence database. The TANDEM application was developed as a freely available database search engine for the proteomics research community. To extend TANDEM as a platform for further research on developing improved database scoring methods, we modified the software to allow users to redefine the scoring function and replace the native TANDEM scoring function while leaving the remaining core application intact. Redefinition is performed at run time so multiple scoring functions are available to be selected and applied from a single search engine binary. We introduce the implementation of the pluggable scoring algorithm and also provide implementations of two TANDEM compatible scoring functions, one previously described scoring function compatible with PeptideProphet and one very simple scoring function that quantitative researchers may use to begin their development. This extension builds on the open-source TANDEM project and will facilitate research into and dissemination of novel algorithms for matching MS/MS spectra to peptide sequences. The pluggable scoring schema is also compatible with related search applications P3 and Hunter, which are part of the X! suite of database matching algorithms. The pluggable scores and the X! suite of applications are all written in C++. AVAILABILITY: Source code for the scoring functions is available from http://proteomics.fhcrc.org

Algorithms↗

PubMed2006

SEBINI: Software Environment for BIological Network Inference.

UNLABELLED: The Software Environment for BIological Network Inference (SEBINI) has been created to provide an interactive environment for the deployment and evaluation of algorithms used to reconstruct the structure of biological regulatory and interaction networks. SEBINI can be used to compare and train network inference methods on artificial networks and simulated gene expression perturbation data. It also allows the analysis within the same framework of experimental high-throughput expression data using the suite of (trained) inference methods; hence SEBINI should be useful to software developers wishing to evaluate, compare, refine or combine inference techniques, and to bioinformaticians analyzing experimental data. SEBINI provides a platform that aids in more accurate reconstruction of biological networks, with less effort, in less time. AVAILABILITY: A demonstration website is located at https://www.emsl.pnl.gov/NIT/NIT.html. The Java source code and PostgreSQL database schema are available freely for non-commercial use.

Algorithms↗

PubMed2006

Model-based boosting in high dimensions.

SUMMARY: The R add-on package mboost implements functional gradient descent algorithms (boosting) for optimizing general loss functions utilizing componentwise least squares, either of parametric linear form or smoothing splines, or regression trees as base learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data. AVAILABILITY: Package mboost is available from the Comprehensive R Archive Network (http://CRAN.R-project.org) under the terms of the General Public Licence (GPL).

Algorithms↗

PubMed2006

Clearcut: a fast implementation of relaxed neighbor joining.

SUMMARY: Clearcut is an open source implementation for the relaxed neighbor joining (RNJ) algorithm. While traditional neighbor joining (NJ) remains a popular method for distance-based phylogenetic tree reconstruction, it suffers from a O(N(3)) time complexity, where N represents the number of taxa in the input. Due to this steep asymptotic time complexity, NJ cannot reasonably handle very large datasets. In contrast, RNJ realizes a typical-case time complexity on the order of N(2)logN without any significant qualitative difference in output. RNJ is particularly useful when inferring a very large tree or a large number of trees. In addition, RNJ retains the desirable property that it will always reconstruct the true tree given a matrix of additive pairwise distances. Clearcut implements RNJ as a C program, which takes either a set of aligned sequences or a pre-computed distance matrix as input and produces a phylogenetic tree. Alternatively, Clearcut can reconstruct phylogenies using an extremely fast standard NJ implementation. AVAILABILITY: Clearcut source code is available for download at: http://bioinformatics.hungry.com/clearcut

Algorithms↗

PubMed2006

PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm.

MOTIVATION: Promoter prediction is important for the analysis of gene regulations. Although a number of promoter prediction algorithms have been reported in literature, significant improvement in prediction accuracy remains a challenge. In this paper, an effective promoter identification algorithm, which is called PromoterExplorer, is proposed. In our approach, we analyze the different roles of various features, that is, local distribution of pentamers, positional CpG island features and digitized DNA sequence, and then combine them to build a high-dimensional input vector. A cascade AdaBoost-based learning procedure is adopted to select the most 'informative' or 'discriminating' features to build a sequence of weak classifiers, which are combined to form a strong classifier so as to achieve a better performance. The cascade structure used for identification can also reduce the false positive. RESULTS: PromoterExplorer is tested based on large-scale DNA sequences from different databases, including the EPD, DBTSS, GenBank and human chromosome 22. Experimental results show that consistent and promising performance can be achieved.

Algorithms↗

PubMed2006

Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis.

MOTIVATION: Metabolic flux analysis of biochemical reaction networks using isotope tracers requires software tools that can analyze the dynamics of isotopic isomer (isotopomer) accumulation in metabolites and reveal the underlying kinetic mechanisms of metabolism regulation. Since existing tools are restricted by the isotopic steady state and remain disconnected from the underlying kinetic mechanisms, we have recently developed a novel approach for the analysis of tracer-based metabolomic data that meets these requirements. The present contribution describes the last step of this development: implementation of (i) the algorithms for the determination of the kinetic parameters and respective metabolic fluxes consistent with the experimental data and (ii) statistical analysis of both fluxes and parameters, thereby lending it a practical application. RESULTS: The C++ applications package for dynamic isotopomer distribution data analysis was supplemented by (i) five distinct methods for resolving a large system of differential equations; (ii) the 'simulated annealing' algorithm adopted to estimate the set of parameters and metabolic fluxes, which corresponds to the global minimum of the difference between the computed and measured isotopomer distributions; and (iii) the algorithms for statistical analysis of the estimated parameters and fluxes, which use the covariance matrix evaluation, as well as Monte Carlo simulations. An example of using this tool for the analysis of (13)C distribution in the metabolites of glucose degradation pathways has demonstrated the evaluation of optimal set of parameters and fluxes consistent with the experimental pattern, their range and statistical significance, and also the advantages of using dynamic rather than the usual steady-state method of analysis. AVAILABILITY: Software is available free from http://www.bq.ub.es/bioqint/selivanov.htm

Algorithms↗

PubMed2006

COPASI--a COmplex PAthway SImulator.

MOTIVATION: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. RESULTS: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. AVAILABILITY: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.

Algorithms↗

PubMed2006

Integration of gel-based proteome data with pProRep.

UNLABELLED: pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. AVAILABILITY: The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.

Computational Biology↗

PubMed2006

BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.

UNLABELLED: BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray datasets with missing data. To evaluate the statistical features of generated Bayesian networks, re-sampling procedures are utilized to yield collections of candidate 1st-order network sets for mining dense coherent sub-networks. AVAILABILITY: The R package and the supplementary documentation are available at http://www.cls.zju.edu.cn/binfo/BNArray/.

Algorithms↗

PubMed2006

CAPS: coevolution analysis using protein sequences.

UNLABELLED: Coevolution Analysis using Protein Sequences (CAPS) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites. Friendly interpretable output files are generated. AVAILABILITY: CAPS version 1 is available at http://bioinf.gen.tcd.ie/~faresm/software/caps/. Distribution versions for Linux/Unix, Mac OS X and Windows operating systems are available, including manual and example files.

Algorithms↗

PubMed2006

Cell++--simulating biochemical pathways.

MOTIVATION: With the generation of a wealth of information, detailing cellular components, their functions and interactions, there is a growing need for the development of new computational tools capable of interpreting these data within spatial and dynamic contexts. Here, we introduce Cell++, a novel stochastic simulation environment with the capacity to study a wide variety of biochemical processes within a spatial context. RESULTS: Focusing on three case studies, we highlight the potential impact of spatial organization in the evolution and engineering of signaling and metabolic pathways. In addition to altering signaling and metabolic efficiency, simulations also demonstrated features consistent with the phenomenon of metabolic channeling. AVAILABILITY: Cell++ is licensed under the GNU general public license (GPL) and has been successfully implemented under Linux and IRIX operating systems. Source code together with a simple tutorial is available at http://www.compsysbio.org/CellSim/.

Biochemistry↗

PubMed2006

P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.

UNLABELLED: The software tool P2BAT provides a massive parallel and user friendly implementation of the PBAT-analysis tools for family-based association tests (FBATs) in large-scale studies, including genome-wide association studies with several thousand subjects. Built on the original PBAT-implementation of the Lange-Van Steen algorithm to bypass the multiple testing problem in family-based association studies, P2BAT integrates all PBAT-analysis tools for binary and complex traits into R and makes them accessible through a user-friendly GUI. The genome-wide analysis tools are fully automated and can be ran massively parallel directly through the GUI. P2BAT is fully documented and contains graphical output tools for time-to-onset analysis. P2BAT also features the ability to test for gene and environment/drug interaction. AVAILABILITY: The P2BAT package is available as the R package 'pbatR' which can be downloaded from http://cran.r-project.org/. The PBAT-software is available at http://www.biostat.harvard.edu/~clange/.

Algorithms↗

PubMed2006

THOR: targeted high-throughput ortholog reconstructor.

Low-coverage genomes (LCGs) are becoming an increasingly important source of data for phylogenetic studies. However, assembly of these genomes is time consuming, difficult and lags behind sequence generation. THOR is a fast, stringent application for targeted reconstruction of sequence orthologs in unassembled LCGs. Using a 4x coverage set of mouse whole-genome sequence reads, THOR could partially or completely reconstruct 416/1000 human promoter ortholog regions in approximately 7.3 min/promoter. THOR's reconstruction rate improves markedly with both higher-coverage, and less divergent target species.

Algorithms↗

PubMed2006

Supporting the SBML layout extension.

MOTIVATION: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted format. SUMMARY: Two modules, SBMLSupportLayout and SBWAutoLayout, support reading, creating, manipulating and writing layout information for biochemical models. SBMLSupportLayout can read, update, add and render model layout information. SBWAutoLayout can automatically layout models, graphically manipulate model layout and generate layout information for models without layout information. AVAILABILITY: SBMLSupportLayout and SBWAutoLayout are distributed with the Systems Biology Workbench (SBW), which can be downloaded from http://www.sys-bio.org. Additionally, their visualization and layout capabilities are available online at http://www.sys-bio.org/Layout. Both modules run on Win32, Linux and the Mac OS X version is forthcoming.

Algorithms↗

PubMed2006

ARIA2: automated NOE assignment and data integration in NMR structure calculation.

UNLABELLED: Modern structural genomics projects demand for integrated methods for the interpretation and storage of nuclear magnetic resonance (NMR) data. Here we present version 2.1 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation. We report on recent developments, most notably a graphical user interface, and the incorporation of the object-oriented data model of the Collaborative Computing Project for NMR (CCPN). The CCPN data model defines a storage model for NMR data, which greatly facilitates the transfer of data between different NMR software packages. AVAILABILITY: A distribution with the source code of ARIA 2.1 is freely available at http://www.pasteur.fr/recherche/unites/Binfs/aria2.

Algorithms↗

PubMed2006

Mosclust: a software library for discovering significant structures in bio-molecular data.

UNLABELLED: The R package mosclust (model order selection for clustering problems) implements algorithms based on the concept of stability for discovering significant structures in bio-molecular data. The software library provides stability indices obtained through different data perturbations methods (resampling, random projections, noise injection), as well as statistical tests to assess the significance of multi-level structures singled out from the data. AVAILABILITY: http://homes.dsi.unimi.it/~valenti/SW/mosclust/download/mosclust_1.0.tar.gz. SUPPLEMENTARY INFORMATION: http://homes.dsi.unimi.it/~valenti/SW/mosclust.

Algorithms↗

PubMed2007

SChiSM2: creating interactive web page annotations of molecular structure models using Jmol.

UNLABELLED: SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with Internet Explorer and Firefox on Windows, Safari and Firefox on Mac OSX and Firefox on Linux. AVAILABILITY: The program can be accessed at the following address: http://ci.vbi.vt.edu/cammer/schism2.html.

Algorithms↗

PubMed2006

CisView: a browser and database of cis-regulatory modules predicted in the mouse genome.

To facilitate the analysis of gene regulatory regions of the mouse genome, we developed a CisView (http://lgsun.grc.nia.nih.gov/cisview), a browser and database of genome-wide potential transcription factor binding sites (TFBSs) that were identified using 134 position-weight matrices and 219 sequence patterns from various sources and were presented with the information about sequence conservation, neighboring genes and their structures, GO annotations, protein domains, DNA repeats and CpG islands. Analysis of the distribution of TFBSs revealed that many TFBSs (N = 145) were over-represented near transcription start sites. We also identified potential cis-regulatory modules (CRMs) defined as clusters of conserved TFBSs in the entire mouse genome. Out of 739 074 CRMs, 157 442 had a significantly higher regulatory potential score than semi-random sequences generated with a 3rd-order Markov process. The CisView browser provides a user-friendly computer environment for studying transcription regulation on a whole-genome scale and can also be used for interpreting microarray experiments and identifying putative targets of transcription factors.

Animals↗