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Current Protocols in Bioinformatics

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https://www.readbyqxmd.com/read/27930809/ascatngs-identifying-somatically-acquired-copy-number-alterations-from-whole-genome-sequencing-data
#1
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
#2
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
#3
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
#4
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
#5
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/27322404/studying-rna-homology-and-conservation-with-infernal-from-single-sequences-to-rna-families
#6
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
#7
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
https://www.readbyqxmd.com/read/27010336/metabolights-an-open-access-database-repository-for-metabolomics-data
#8
Namrata S Kale, Kenneth Haug, Pablo Conesa, Kalaivani Jayseelan, Pablo Moreno, Philippe Rocca-Serra, Venkata Chandrasekhar Nainala, Rachel A Spicer, Mark Williams, Xuefei Li, Reza M Salek, Julian L Griffin, Christoph Steinbeck
MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e...
March 24, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27010335/introduction-to-cheminformatics
#9
David S Wishart
Cheminformatics is a field of information technology that focuses on the collection, storage, analysis, and manipulation of chemical data. The chemical data of interest typically includes information on small molecule formulas, structures, properties, spectra, and activities (biological or industrial). Cheminformatics originally emerged as a vehicle to help the drug discovery and development process, however cheminformatics now plays an increasingly important role in many areas of biology, chemistry, and biochemistry...
March 24, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27010334/using-psea-quant-for-protein-set-enrichment-analysis-of-quantitative-mass-spectrometry-based-proteomics
#10
Mathieu Lavallée-Adam, John R Yates
PSEA-Quant analyzes quantitative mass spectrometry-based proteomics datasets to identify enrichments of annotations contained in repositories such as the Gene Ontology and Molecular Signature databases. It allows users to identify the annotations that are significantly enriched for reproducibly quantified high abundance proteins. PSEA-Quant is available on the Web and as a command-line tool. It is compatible with all label-free and isotopic labeling-based quantitative proteomics methods. This protocol describes how to use PSEA-Quant and interpret its output...
March 24, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27010333/uniprot-tools
#11
Sangya Pundir, Maria J Martin, Claire O'Donovan
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides three main tools. These are the 'BLAST' tool for sequence similarity searching, the 'Align' tool for multiple sequence alignment, and the 'Retrieve/ID Mapping' tool for using a list of identifiers to retrieve UniProtKB proteins and to convert database identifiers from UniProt to external databases or vice versa...
March 24, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27603023/using-metaboanalyst-3-0-for-comprehensive-metabolomics-data-analysis
#12
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...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27603022/tempest-accelerated-ms-ms-database-search-software-for-heterogeneous-computing-platforms
#13
Mark E Adamo, Scott A Gerber
MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27603021/obtaining-mirna-target-interaction-information-from-mirwalk2-0
#14
Alisha Parveen, Norbert Gretz, Harsh Dweep
miRWalk2.0 (http://zmf.umm.uni-heidelberg.de/mirwalk2) is a freely accessible, regularly updated comprehensive archive supplying the largest available collection of predicted and experimentally verified miRNA-target interactions, with various novel and unique features to assist the scientific community. Approximately 949 million interactions between 11,748 miRNAs, 308,700 genes, and 68,460 lncRNAs are documented in miRWalk2.0 with 5,146,217 different kinds of identifiers to offer a one-stop site to collect an abundance of information...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27603020/diana-tarbase-and-diana-suite-tools-studying-experimentally-supported-microrna-targets
#15
Maria D Paraskevopoulou, Ioannis S Vlachos, Artemis G Hatzigeorgiou
microRNAs (miRNAs) are short non-coding RNAs (∼22 nts) present in animals, plants, and viruses. They are considered central post-transcriptional regulators of gene expression and are key components in a great number of physiological and pathological conditions. The accurate characterization of their targets is considered essential to a series of applications and basic or applied research settings. DIANA-TarBase (http://www.microrna.gr/tarbase) was initially launched in 2006. It is a reference repository indexing experimentally derived miRNA-gene interactions in different cell types, tissues, and conditions across numerous species...
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...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322407/inference-of-episodic-changes-in-natural-selection-acting-on-protein-coding-sequences-via-codeml
#17
Joseph P Bielawski, Jennifer L Baker, Joseph Mingrone
This unit provides protocols for using the CODEML program from the PAML package to make inferences about episodic natural selection in protein-coding sequences. The protocols cover inference tasks such as maximum likelihood estimation of selection intensity, testing the hypothesis of episodic positive selection, and identifying sites with a history of episodic evolution. We provide protocols for using the rich set of models implemented in CODEML to assess robustness, and for using bootstrapping to assess if the requirements for reliable statistical inference have been met...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322406/comparative-protein-structure-modeling-using-modeller
#18
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...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322405/using-drugbank-for-in-silico-drug-exploration-and-discovery
#19
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...
2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27322403/the-genecards-suite-from-gene-data-mining-to-disease-genome-sequence-analyses
#20
Gil Stelzer, Naomi Rosen, Inbar Plaschkes, Shahar Zimmerman, Michal Twik, Simon Fishilevich, Tsippi Iny Stein, Ron Nudel, Iris Lieder, Yaron Mazor, Sergey Kaplan, Dvir Dahary, David Warshawsky, Yaron Guan-Golan, Asher Kohn, Noa Rappaport, Marilyn Safran, Doron Lancet
GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression...
2016: Current Protocols in Bioinformatics
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