Genomes and Genes
Summary: Sequential operating programs and data which instruct the functioning of a digital computer.
- Aubertot J, Robin M. Injury Profile SIMulator, a qualitative aggregative modelling framework to predict crop injury profile as a function of cropping practices, and the abiotic and biotic environment. I. Conceptual bases. PLoS ONE. 2013;8:e73202 pubmed publisher..In addition, IPSIM could also be used to help make diagnoses on commercial fields. It is important to point out that the presented concepts are not crop- or pest-specific and that IPSIM can be used on any crop. ..
- Liu X, Han S, Wang Z, Gelernter J, Yang B. Variant callers for next-generation sequencing data: a comparison study. PLoS ONE. 2013;8:e75619 pubmed publisher..87% and 99.82%, respectively. In conclusion, GATK showed several advantages over other variant callers for general purpose NGS analyses. The GATK pipelines we developed perform very well. ..
- Contreras Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013;79:7696-701 pubmed publisherGET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians...
- Tang Q, Zhang C. Data Processing System (DPS) software with experimental design, statistical analysis and data mining developed for use in entomological research. Insect Sci. 2013;20:254-60 pubmed publisherA comprehensive but simple-to-use software package called DPS (Data Processing System) has been developed to execute a range of standard numerical analyses and operations used in experimental design, statistics and data mining...
- Steijger T, Abril J, Engström P, Kokocinski F, Hubbard T, Guigo R, et al. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013;10:1177-84 pubmed publisher..Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data. ..
- Overbeek R, Olson R, Pusch G, Olsen G, Davis J, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:D206-14 pubmed publisher..To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources. ..
- Ilie L, Molnar M. RACER: Rapid and accurate correction of errors in reads. Bioinformatics. 2013;29:2490-3 pubmed publisher..We propose RACER (Rapid and Accurate Correction of Errors in Reads), a new software program for correcting errors in sequencing data...
- Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312-3 pubmed publisher..In addition, an up-to-date 50-page user manual covering all new RAxML options is available. ..
- Kajan L, Hopf T, Kalas M, Marks D, Rost B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics. 2014;15:85 pubmed publisher..On top, EVfold-mfDCA depends on proprietary software. Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV...
- Jaiswal V, Chanumolu S, Gupta A, Chauhan R, Rout C. Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics. 2013;14:211 pubmed publisher..The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development...
- Liao Y, Smyth G, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923-30 pubmed publisher..featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
- Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes Carter F, et al. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014;42:D358-63 pubmed publisher..Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). ..
- Engström P, Steijger T, Sipos B, Grant G, Kahles A, Rätsch G, et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods. 2013;10:1185-91 pubmed publisher..To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets...
- Asfour A, Raoof K, Yonnet J. Software Defined Radio (SDR) and Direct Digital Synthesizer (DDS) for NMR/MRI instruments at low-field. Sensors (Basel). 2013;13:16245-62 pubmed publisher..electronics is based on the use of three key elements: a Direct Digital Synthesizer (DDS) for pulse generation, a Software Defined Radio (SDR) for a digital receiving of NMR signals and a Digital Signal Processor (DSP) for system ..
- Lagerstedt I, Moore W, Patwardhan A, Sanz GarcÃa E, Best C, Swedlow J, et al. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. J Struct Biol. 2013;184:173-81 pubmed publisher..the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives...
- Forkert N, Cheng B, Kemmling A, Thomalla G, Fiehler J. ANTONIA perfusion and stroke. A software tool for the multi-purpose analysis of MR perfusion-weighted datasets and quantitative ischemic stroke assessment. Methods Inf Med. 2014;53:469-81 pubmed publisherThe objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of ..
- Nawrocki E, Eddy S. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933-5 pubmed publisher..Documentation includes a user's guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. email@example.com
- Müller S, Rycak L, Winter P, Kahl G, Koch I, Rotter B. omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinformatics. 2013;29:2651-2 pubmed publisher..The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/. ..
- Do C, Waples R, Peel D, Macbeth G, Tillett B, Ovenden J. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data. Mol Ecol Resour. 2014;14:209-14 pubmed publisherNeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file...
- Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, et al. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics. 2013;29:2320-6 pubmed publisher..caspo is freely available for download (license GPLv3) and as a web service at http://caspo.genouest.org/. Supplementary materials are available at Bioinformatics online. firstname.lastname@example.org. ..
- Criscuolo A, Brisse S. AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics. 2013;102:500-6 pubmed publisher..The program is freely available at ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/. ..
- Kumar D, Yadav A, Kadimi P, Nagaraj S, Grimmond S, Dash D. Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics. 2013;12:3388-97 pubmed publisher..japonicum and presents an unparalleled utility of proteogenomic analyses and versatility of GenoSuite for annotating prokaryotic genomes including pathogens. ..
- Shannon P, GRIMES M, Kutlu B, Bot J, Galas D. RCytoscape: tools for exploratory network analysis. BMC Bioinformatics. 2013;14:217 pubmed publisher..in statistical power and data-handling facilities) and Cytoscape (powerful network visualization and analysis software)...
- Lange S, Alkhnbashi O, Rose D, Will S, Backofen R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 2013;41:8034-44 pubmed publisher..informatik.uni-freiburg.de/CRISPRmap. ..
- Behr J, Kahles A, Zhong Y, Sreedharan V, Drewe P, Rätsch G. MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics. 2013;29:2529-38 pubmed publisher..MITIE is implemented in C++ and is available from http://bioweb.me/mitie under the GPL license. ..
- Kellis M, Wold B, Snyder M, Bernstein B, Kundaje A, Marinov G, et al. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014;111:6131-8 pubmed publisher..Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease. ..
- Grau J, Posch S, Grosse I, Keilwagen J. A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res. 2013;41:e197 pubmed publisher..We also observe that modeling intra-motif dependencies may increase accuracy, which indicates that more complex motif models are a worthwhile field of research. ..
- Grau J, Boch J, Posch S. TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics. 2013;29:2931-2 pubmed publisher..TALENoffer is available as a command line program from http://www.jstacs.de/index.php/TALENoffer and as a Galaxy server at http://galaxy.informatik.uni-halle.de. email@example.com ..
- Egea J, Henriques D, Cokelaer T, Villaverde A, MacNamara A, Danciu D, et al. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics. 2014;15:136 pubmed publisher..It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods. ..
- Estévez Santiago R, Beltrán de Miguel B, Cuadrado Vives C, Olmedilla Alonso B. Software application for the calculation of dietary intake of individual carotenoids and of its contribution to vitamin A intake. Nutr Hosp. 2013;28:823-9 pubmed publisherThe software applications utilized to assess dietary intake usually focus on macro- and micronutrients, but not on other components of the diet with potential beneficial effects on health, which include the carotenoids...
- Kristensen V, Lingjærde O, Russnes H, Vollan H, Frigessi A, Børresen Dale A. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer. 2014;14:299-313 pubmed publisher..The objectives, methods and computational tools of integrative genomics that are available to date are reviewed here, as is their implementation in cancer research. ..
- Jones P, Binns D, Chang H, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236-40 pubmed publisher..Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan...
- Paulson J, Stine O, Bravo H, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200-2 pubmed publisher..Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field. ..
- Kuś R, Różański P, Durka P. Multivariate matching pursuit in optimal Gabor dictionaries: theory and software with interface for EEG/MEG via Svarog. Biomed Eng Online. 2013;12:94 pubmed publisher..We implement this construction in a freely available software for MP decomposition of multivariate time series, with a user friendly interface via the Svarog package (Signal ..
- Karolchik D, Barber G, Casper J, Clawson H, Cline M, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42:D764-70 pubmed publisher..New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants ..
- Tomasini N, Lauthier J, Llewellyn M, Diosque P. MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms. Infect Genet Evol. 2013;20:188-96 pubmed publisher..Here we present novel software for MLST data analysis tailored towards diploid Eukaryotes: MLSTest...
- Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D. GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures. PLoS ONE. 2013;8:e76911 pubmed publisher..computers to more advanced symmetric multiprocessing (SMP), offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential...
- Markowitz V, Chen I, Chu K, Szeto E, Palaniappan K, Pillay M, et al. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 2014;42:D568-73 pubmed publisher..jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp). ..
- Bucher E, Brooks K, Verber M, Keithley R, Owesson White C, Carroll S, et al. Flexible software platform for fast-scan cyclic voltammetry data acquisition and analysis. Anal Chem. 2013;85:10344-53 pubmed publisher..HDCV is an electrochemical software suite that includes data acquisition and analysis programs...
- Tarvainen M, Niskanen J, Lipponen J, Ranta aho P, Karjalainen P. Kubios HRV--heart rate variability analysis software. Comput Methods Programs Biomed. 2014;113:210-20 pubmed publisherKubios HRV is an advanced and easy to use software for heart rate variability (HRV) analysis. The software supports several input data formats for electrocardiogram (ECG) data and beat-to-beat RR interval data...
- Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher C, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2014;42:D459-71 pubmed publisher..enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
- Tamborero D, González Pérez A, Lopez Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013;29:2238-44 pubmed publisher..OncodriveCLUST has been implemented as a Python script and is freely available from http://bg.upf.edu/oncodriveclust firstname.lastname@example.org or email@example.com Supplementary data are available at Bioinformatics online. ..
- Anders S, McCarthy D, Chen Y, Okoniewski M, Smyth G, Huber W, et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc. 2013;8:1765-86 pubmed publisher..differential expression analysis workflow largely based on the free open-source R language and Bioconductor software and, in particular, on two widely used tools, DESeq and edgeR. Hands-on time for typical small experiments (e.g...
- Omasits U, Ahrens C, Müller S, Wollscheid B. Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. 2014;30:884-6 pubmed publisher..The Protter web application is available at http://wlab.ethz.ch/protter. Source code and installation instructions are available at http://ulo.github.io/Protter/. firstname.lastname@example.org Supplementary data are available at Bioinformatics online. ..
- Young B, Loewen C. Balony: a software package for analysis of data generated by synthetic genetic array experiments. BMC Bioinformatics. 2013;14:354 pubmed publisher..We have designed software that is able to analyze virtually any image of regularly arrayed colonies and allows the user significant ..
- Zimin A, Marçais G, Puiu D, Roberts M, Salzberg S, Yorke J. The MaSuRCA genome assembler. Bioinformatics. 2013;29:2669-77 pubmed publisher..We call our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced 'mazurka')...
- Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013;34:E2393-402 pubmed publisher..dbNSFP v2.0 is freely available for download at http://sites.google.com/site/jpopgen/dbNSFP. ..
- Santos A, Barbosa E, Fiaux K, Zurita Turk M, Chaitankar V, Kamapantula B, et al. PANNOTATOR: an automated tool for annotation of pan-genomes. Genet Mol Res. 2013;12:2982-9 pubmed publisher..PANNOTATOR provides fast and reliable pan-genome annotation; thereby allowing us to maintain the research focus on the main genotype differences between strains. ..
- Comeau D, Islamaj Doğan R, Ciccarese P, Cohen K, Krallinger M, Leitner F, et al. BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013;2013:bat064 pubmed publisher..We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net/ ..
- Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, et al. E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res. 2013;41:e190 pubmed publisher..An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future. ..