DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

Summary: DeconMSn accurately determines the monoisotopic massand charge state of parent ions from high-resolution tandemmass spectrometry data, offering significant improvement forLTQ_FT and LTQ_Orbitrap instruments over the commercially deliveredThermo Fisher Scientific's extract_msn tool. Optimal parention mass tolerance values can be determined using accurate massinformation, thus improving peptide identifications for high-massmeasurement accuracy experiments. For low-resolution data fromLCQ and LTQ instruments, DeconMSn incorporates a support-vector-machine-basedcharge detection algorithm that identifies the most likely chargeof a parent species through peak characteristics of its fragmentationpattern. Availability: http://ncrr.pnl.gov/software/ or http://www.proteomicsresource.org/ Contact: rds{at}pnl.gov Supplementary information: PowerPoint presentation/Poster onhttp://ncrr.pnl.gov/software/. Associate Editor: Alfonso Valencia     

A multivariate test of association

Summary: Although genetic association studies often test multiple,related phenotypes, few formal multivariate tests of associationare available. We describe a test of association that can beefficiently applied to large population-based designs. Availability: A C++ implementation can be obtained from theauthors. Contact: manuel.ferreira{at}qimr.edu.au Supplementary information: Supplementary figures are availableat Bioinformatics online. Associate Editor: Alex Bateman     

CRONOS: the cross-reference navigation server

Summary: Cross-mapping of gene and protein identifiers betweendifferent databases is a tedious and time-consuming task. Toovercome this, we developed CRONOS, a cross-reference serverthat contains entries from five mammalian organisms presentedby major gene and protein information resources. Sequence similarityanalysis of the mapped entries shows that the cross-referencesare highly accurate. In total, up to 18 different identifiertypes can be used for identification of cross-references. Thequality of the mapping could be improved substantially by exclusionof ambiguous gene and protein names which were manually validated.Organism-specific lists of ambiguous terms, which are valuablefor a variety of bioinformatics applications like text miningare available for download. Availability: CRONOS is freely available to non-commercial usersat http://mips.gsf.de/genre/proj/cronos/index.html, web servicesare available at http://mips.gsf.de/CronosWSService/CronosWS?wsdl. Contact: brigitte.waegele{at}helmholtz-muenchen.de Supplementary information: Supplementary data are availableat Bioinformatics online. The online Supplementary Materialcontains all figures and tables referenced by this article. Associate Editor: Martin Bishop     

PQuad--a visual analysis platform for proteomic data exploration of microbial organisms

Summary: The visual Platform for Proteomics Peptide and Proteindata exploration (PQuad) is a multi-resolution environment thatvisually integrates genomic and proteomic data for prokaryoticsystems, overlays categorical annotation and compares differentialexpression experiments. PQuad requires Java 1.5 and has beentested to run across different operating systems. Availability: http://ncrr.pnl.gov/software Contact: bobbie-jo.webb-robertson{at}pnl.gov Associate Editor: Thomas Lengauer     

PDBML: the representation of archival macromolecular structure data in XML

Summary: The Protein Data Bank (PDB) has recently released versionsof the PDB Exchange dictionary and the PDB archival data filesin XML format collectively named PDBML. The automated generationof these XML files is driven by the data dictionary infrastructurein use at the PDB. The correspondences between the PDB dictionaryand the XML schema metadata are described as well as the XMLrepresentations of PDB dictionaries and data files. Availability: The current software translated XML schema fileis located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd,and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/.PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML Contact: jwest{at}rcsb.rutgers.edu     

Genetic association analysis with FAMHAP: a major program update

Summary: FAMHAP is an established software for haplotype associationanalysis of nuclear families. We have released a major updatethat comprises various new features for case-control data. Furthermore,weprovide an additional program runFamhap that allows usersto start the same method repeatedly for varying sets of geneticmarkers. In addition, a platform-independent graphical userinterface (GUI) was developed to simplify the usage of bothFAMHAP and runFamhap. The runFamhap program greatly facilitatesthe application of FAMHAP to genome-wide association studies(GWAS) and supports flexible genome-wide haplotype analysis.As an example, we describe application to HapMap data. Availability: The software is available at http://famhap.meb.uni-bonn.de Contact: herold{at}imbie.meb.uni-bonn.de; becker{at}imbie.meb.uni-bonn.de Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Alex Bateman     

BicOverlapper: a tool for bicluster visualization

Summary: BicOverlapper is a tool to visualize biclusters fromgene-expression matrices in a way that helps to compare biclusteringmethods, to unravel trends and to highlight relevant genes andconditions. A visual approach can complement biological andstatistical analysis and reduce the time spent by specialistsinterpreting the results of biclustering algorithms. The techniqueis based on a force-directed graph where biclusters are representedas flexible overlapped groups of genes and conditions. Availability: The BicOverlapper software and supplementary materialare available at http://vis.usal.es/bicoverlapper Contact: rodri{at}usal.es Associate Editor: John Quackenbush The first two authors should be reported as joint first authors.     

The Taverna Interaction Service: enabling manual interaction in workflows

Summary: Taverna is an application that eases the integrationof tools and databases for life science research by the constructionof workflows. The Taverna Interaction Service extends the functionalityof Taverna by defining human interaction within a workflow andacting as a mediation layer between the automated workflow engineand one or more users. Availability: Taverna, the Interaction Service plug-in and webapplication are available as open source and can be downloadedfrom http://taverna.sourceforge.net/ Contact: taverna-users{at}lists.sourceforge.net Associate Editor: John Quackenbush     

Using flowViz to visualize flow cytometry data

Summary: Automated analysis of flow cytometry (FCM) data isessential for it to become successful as a high throughput technology.We believe that the principles of Trellis graphics can be adaptedto provide useful visualizations that can aid such automation.In this article, we describe the R/Bioconductor package flowVizthat implements such visualizations. Availability: flowViz is available as an R package from theBioconductor project: http://bioconductor.org Contact: dsarkar{at}fhcrc.org Associate Editor: Olga Troyanskaya     

Visualization of unfavorable interactions in protein folds

Summary: Three dimensional structures of proteins contain errorswhich often originate from limitations of the experimental techniquesemployed. Such errors frequently result in unfavorable atomicinteractions. Here we present a new web service, called InteractionViewer, for the visualization and correction of such errors.We show how the Interaction Viewer is used in combination withthe NQ-Flipper service to spot strained asparagine and glutaminerotamers and we emphasize the convenience of this service incorrecting such errors. Availability: The web service is integrated with the NQ-Flipperservice and accessible at http://flipper.services.came.sbg.ac.at Contact: sippl{at}came.sbg.ac.at Associate Editor: Anna Tramontano     

GENESIS: genome evolution scenarios

Summary: We implemented a software tool called GENESIS for threedifferent genome rearrangement problems: Sorting a unichromosomalgenome by weighted reversals and transpositions (SwRT), sortinga multichromosomal genome by reversals, translocations, fusionsand fissions (SRTl), and sorting a multichromosomal genome byweighted reversals, translocations, fusions, fissions and transpositions(SwRTTl). Availability: Source code can be obtained by the authors, oruse the web interface http://www.uni-ulm.de/in/theo/research/genesis.html Contact: simon.gog{at}uni-ulm.de Associate Editor: Chris Stoeckert     

GENOME: a rapid coalescent-based whole genome simulator

Summary: GENOME proposes a rapid coalescent-based approach tosimulate whole genome data. In addition to features of standardcoalescent simulators, the program allows for recombinationrates to vary along the genome and for flexible population histories.Within small regions, we have evaluated samples simulated byGENOME to verify that GENOME provides the expected LD patternsand frequency spectra. The program can be used to study thesampling properties of any statistic for a whole genome study. Availability: The program and C++ source code are availableonline at http://www.sph.umich.edu/csg/liang/genome/ Contact: lianglim{at}umich.edu Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Interactive visualization software for exploring phylogenetic trees and clades

Summary: The Summary Tree Explorer (STE) is a Java applicationfor interactively exploring sets of phylogenetic trees usingtwo coupled representations: a node-and-link diagram and a textuallist of common clades. Selection, pruning, filtering or re-rootingin one representation is immediately reflected in the other.While summary trees are more effective at showing the relationshipamong clades, they can only show a consistent subset of thosethat appear in the textual list. Working with both representationsmitigates the disadvantages of having to choose just one. Availability: STE, along with several sample datasets, is availableat http://cityscape.inf.cs.cmu.edu/phylogeny/ Contact: mad{at}cs.cmu.edu Associate Editor: Martin Bishop     

TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers

Summary: Selection of optimal biomarkers for the identificationof different operational taxonomic units (OTUs) may be a hardand tedious task, especially when phylogenetic trees for multiplegenes need to be compared. With TaxonGap we present a noveland easy-to-handle software tool that allows visual comparisonof the discriminative power of multiple biomarkers for a setof OTUs. The compact graphical output allows for easy comparisonand selection of individual biomarkers. Availability: Graphical User Interface; Executable JAVA archivefile, source code, supplementary information and sample filescan be downloaded from the website: http://www.kermit.ugent.be/taxongap Contact: Bram.Slabbinck{at}UGent.be Associate Editor: John Quackenbush