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Current Protocols in Bioinformatics

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https://www.readbyqxmd.com/read/28654729/signor-a-database-of-causal-relationships-between-biological-entities-a-short-guide-to-searching-and-browsing
#1
Prisca Lo Surdo, Alberto Calderone, Gianni Cesareni, Livia Perfetto
SIGNOR (http://signor.uniroma2.it), the SIGnaling Network Open Resource, is a database designed to store experimentally validated causal interactions, i.e., interactions where a source entity has a regulatory effect (up-regulation, down-regulation, etc.) on a second target entity. SIGNOR acts both as a source of signaling information and a support for data analysis, modeling, and prediction. A user-friendly interface features the ability to search entries for any given protein or group of proteins and to display their interactions graphically in a network view...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654728/finding-similar-nucleotide-sequences-using-network-blast-searches
#2
Istvan Ladunga
The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654727/using-the-noncode-database-resource
#3
Li Xiyuan, Bu Dechao, Sun Liang, Wu Yang, Fang Shuangsang, Li Hui, Luo Haitao, Luo Chunlong, Fang Wenzheng, Chen Runsheng, Zhao Yi
NONCODE is a comprehensive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNA genes), and thus NONCODE is essential to modern biological and medical research. Scientists are producing a flood of new data from which new lncRNA genes and lncRNA-disease relationships are continually being identified. NONCODE assimilates such information from a wide variety of sources including published articles, RNA-seq data, micro-array data and databases on genetic variation (dbSNP) and genome-wide associations (GWAS)...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654726/exploring-short-linear-motifs-using-the-elm-database-and-tools
#4
Marc Gouw, Hugo Sámano-Sánchez, Kim Van Roey, Francesca Diella, Toby J Gibson, Holger Dinkel
The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654725/searching-online-mendelian-inheritance-in-man-omim-a-knowledgebase-of-human-genes-and-genetic-phenotypes
#5
Joanna S Amberger, Ada Hamosh
Online Mendelian Inheritance in Man (OMIM) at OMIM.org is the primary repository of comprehensive, curated information on genes and genetic phenotypes and the relationships between them. This unit provides an overview of the types of information in OMIM and optimal strategies for searching and retrieving the information. OMIM.org has links to many related and complementary databases, providing easy access to more information on a topic. The relationship between genes and genetic disorders is highlighted in this unit...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654712/identifying-significantly-impacted-pathways-and-putative-mechanisms-with-ipathwayguide
#6
Sidra Ahsan, Sorin Drăghici
iPathwayGuide is a gene expression analysis tool that provides biological context and inferences from data generated by high-throughput sequencing. iPathwayGuide utilizes a systems biology approach to identify significantly impacted signaling pathways, Gene Ontology terms, disease processes, predicted microRNAs, and putative mechanisms based on the given differential expression signature. By using a novel analytical approach called Impact Analysis, iPathwayGuide considers the role, position, and relationships of each gene within a pathway, which results in a significant reduction in false positives, as well as a better ability to identify the truly impacted pathways and putative mechanisms that can explain all measured gene expression changes...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28463400/using-3drna-for-rna-3-d-structure-prediction-and-evaluation
#7
Jian Wang, Yi Xiao
This unit describes how to use 3dRNA to predict RNA 3-D structures from their sequences and secondary (2-D) structures, and how to use 3dRNAscore to evaluate the predicted structures. The predicted RNA 3-D structures can be used to predict or understand their functions and can also be used to find the interactions between the RNA and other molecules. © 2017 by John Wiley & Sons, Inc.
May 2, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28463399/phylogenetic-inference-using-revbayes
#8
Sebastian Höhna, Michael J Landis, Tracy A Heath
Bayesian phylogenetic inference aims to estimate the evolutionary relationships among different lineages (species, populations, gene families, viral strains, etc.) in a model-based statistical framework that uses the likelihood function for parameter estimates. In recent years, evolutionary models for Bayesian analysis have grown in number and complexity. RevBayes uses a probabilistic-graphical model framework and an interactive scripting language for model specification to accommodate and exploit model diversity and complexity within a single software package...
May 2, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28463398/using-funseq2-for-coding-and-non-coding-variant-annotation-and-prioritization
#9
Priyanka Dhingra, Yao Fu, Mark Gerstein, Ekta Khurana
The identification of non-coding drivers remains a challenge and bottleneck for the use of whole-genome sequencing in the clinic. FunSeq2 is a computational tool for annotation and prioritization of somatic mutations in coding and non-coding regions. It integrates a data context made from large-scale genomic datasets and uses a high-throughput variant prioritization pipeline. This unit provides guidelines for installing and running FunSeq2 to (a) annotate and prioritize variants, (b) incorporate user-defined annotations, and (c) detect differential gene expression...
May 2, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27930809/ascatngs-identifying-somatically-acquired-copy-number-alterations-from-whole-genome-sequencing-data
#10
Keiran M Raine, Peter Van Loo, David C Wedge, David Jones, Andrew Menzies, Adam P Butler, Jon W Teague, Patrick Tarpey, Serena Nik-Zainal, Peter J Campbell
We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27930808/searching-the-mouse-genome-informatics-mgi-resources-for-information-on-mouse-biology-from-genotype-to-phenotype
#11
David R Shaw
The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, vertebrate homologies, SNPs, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Dictionary, the Mammalian Phenotype Ontology, and the Gene Ontologies...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27930807/exploring-flybase-data-using-quicksearch
#12
Steven J Marygold, Giulia Antonazzo, Helen Attrill, Marta Costa, Madeline A Crosby, Gilberto Dos Santos, Joshua L Goodman, L Sian Gramates, Beverley B Matthews, Alix J Rey, Jim Thurmond
FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27930806/the-search-engine-for-multi-proteoform-complexes-an-online-tool-for-the-identification-and-stoichiometry-determination-of-protein-complexes
#13
Owen S Skinner, Luis F Schachner, Neil L Kelleher
Recent advances in top-down mass spectrometry using native electrospray now enable the analysis of intact protein complexes with relatively small sample amounts in an untargeted mode. Here, we describe how to characterize both homo- and heteropolymeric complexes with high molecular specificity using input data produced by tandem mass spectrometry of whole protein assemblies. The tool described is a "search engine for multi-proteoform complexes," (SEMPC) and is available for free online. The output is a list of candidate multi-proteoform complexes and scoring metrics, which are used to define a distinct set of one or more unique protein subunits, their overall stoichiometry in the intact complex, and their pre- and post-translational modifications...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27930805/cgpcavemanwrapper-simple-execution-of-caveman-in-order-to-detect-somatic-single-nucleotide-variants-in-ngs-data
#14
David Jones, Keiran M Raine, Helen Davies, Patrick S Tarpey, Adam P Butler, Jon W Teague, Serena Nik-Zainal, Peter J Campbell
CaVEMan is an expectation maximization-based somatic substitution-detection algorithm that is written in C. The algorithm analyzes sequence data from a test sample, such as a tumor relative to a reference normal sample from the same patient and the reference genome. It performs a comparative analysis of the tumor and normal sample to derive a probabilistic estimate for putative somatic substitutions. When combined with a set of validated post-hoc filters, CaVEMan generates a set of somatic substitution calls with high recall and positive predictive value...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27603023/using-metaboanalyst-3-0-for-comprehensive-metabolomics-data-analysis
#15
Jianguo Xia, David S Wishart
MetaboAnalyst (http://www.metaboanalyst.ca) is a comprehensive Web application for metabolomic data analysis and interpretation. MetaboAnalyst handles most of the common metabolomic data types from most kinds of metabolomics platforms (MS and NMR) for most kinds of metabolomics experiments (targeted, untargeted, quantitative). In addition to providing a variety of data processing and normalization procedures, MetaboAnalyst also supports a number of data analysis and data visualization tasks using a range of univariate, multivariate methods such as PCA (principal component analysis), PLS-DA (partial least squares discriminant analysis), heatmap clustering and machine learning methods...
September 7, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27603019/using-the-tools-and-resources-of-the-rcsb-protein-data-bank
#16
Luigi Di Costanzo, Sutapa Ghosh, Christine Zardecki, Stephen K Burley
The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata...
September 7, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322406/comparative-protein-structure-modeling-using-modeller
#17
Benjamin Webb, Andrej Sali
Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications...
June 20, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322405/using-drugbank-for-in-silico-drug-exploration-and-discovery
#18
David S Wishart, Anthony Wu
DrugBank is a fully curated drug and drug target database that contains 8174 drug entries including 1944 FDA approved small-molecule drugs, 198 FDA-approved biotech (protein/peptide) drugs, 93 nutraceuticals, and over 6000 experimental drugs. Additionally, 4300 non-redundant protein (i.e., drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. DrugBank is primarily focused on providing both the query/search tools and biophysical data needed to facilitate drug discovery and drug development...
June 20, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322404/studying-rna-homology-and-conservation-with-infernal-from-single-sequences-to-rna-families
#19
Lars Barquist, Sarah W Burge, Paul P Gardner
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary structure prediction and search remain difficult...
June 20, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27010337/finding-protein-and-nucleotide-similarities-with-fasta
#20
William R Pearson
The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity...
March 24, 2016: Current Protocols in Bioinformatics
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