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Current Protocols in Bioinformatics

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https://www.readbyqxmd.com/read/29927072/non-coding-rna-analysis-using-the-rfam-database
#1
Ioanna Kalvari, Eric P Nawrocki, Joanna Argasinska, Natalia Quinones-Olvera, Robert D Finn, Alex Bateman, Anton I Petrov
Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site...
June 5, 2018: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29927080/spin-submitting-sequences-determined-at-protein-level-to-uniprot
#2
Klemens Pichler, Kate Warner, Michele Magrane
Public availability of biological sequences is essential for their widespread access and use by the research community. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and functional data. While most protein sequences entering UniProt are imported from other source databases containing nucleotide or 3-D structure data, protein sequences determined at the protein level can be submitted directly to UniProt. To this end, UniProt provides a Web interface called SPIN. This service enables researchers to make their de novo-sequenced proteins available to the scientific community and acquire UniProt accession numbers for use in publications...
May 25, 2018: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29927076/the-gwips-viz-browser
#3
Stephen J Kiniry, Audrey M Michel, Pavel V Baranov
GWIPS-viz is a publicly available browser that provides Genome Wide Information on Protein Synthesis through the visualization of ribosome profiling data. Ribosome profiling (Ribo-seq) is a high-throughput technique which isolates fragments of messenger RNA that are protected by the ribosome. The alignment of the ribosome-protected fragments or footprint sequences to the corresponding reference genome and their visualization using GWIPS-viz allows for unique insights into the genome loci that are expressed as potentially translated RNA...
May 16, 2018: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29927069/using-lichee-and-bamse-for-reconstructing-cancer-phylogenetic-trees
#4
Camir Ricketts, Victoria Popic, Hosein Toosi, Iman Hajirasouliha
The reconstruction of cancer phylogeny trees and quantifying the evolution of the disease is a challenging task. LICHeE and BAMSE are two computational tools designed and implemented recently for this purpose. They both utilize estimated variant allele fraction of somatic mutations across multiple samples to infer the most likely cancer phylogenies. This unit provides extensive guidelines for installing and running both LICHeE and BAMSE. © 2018 by John Wiley & Sons, Inc.
May 16, 2018: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/30008982/emdb-web-resources
#5
Sanja Abbott, Andrii Iudin, Paul K Korir, Sriram Somasundharam, Ardan Patwardhan
The Electron Microscopy Data Bank (EMDB; http://emdb-empiar.org) is a global openly-accessible archive of biomolecular and cellular 3D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualising EMDB structures, statistically analysing EMDB content and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive and a form-based search...
March 2018: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29220078/using-the-seven-bridges-cancer-genomics-cloud-to-access-and-analyze-petabytes-of-cancer-data
#6
Raunaq Malhotra, Isheeta Seth, Erik Lehnert, Jing Zhao, Gaurav Kaushik, Elizabeth H Williams, Anurag Sethi, Brandi N Davis-Dusenbery
Next-generation sequencing has produced petabytes of data, but accessing and analyzing these data remain challenging. Traditionally, researchers investigating public datasets like The Cancer Genome Atlas (TCGA) would download the data to a high-performance cluster, which could take several weeks even with a highly optimized network connection. The National Cancer Institute (NCI) initiated the Cancer Genomics Cloud Pilots program to provide researchers with the resources to process data with cloud computational resources...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29220077/using-the-arabidopsis-information-resource-tair-to-find-information-about-arabidopsis-genes
#7
Leonore Reiser, Shabari Subramaniam, Donghui Li, Eva Huala
The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, orthologs, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web-based search and display tools...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29220076/the-hmmer-web-server-for-protein-sequence-similarity-search
#8
Ananth Prakash, Matt Jeffryes, Alex Bateman, Robert D Finn
Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29220075/protein-3d-structure-and-electron-microscopy-map-retrieval-using-3d-surfer2-0-and-em-surfer
#9
Xusi Han, Qing Wei, Daisuke Kihara
With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29220074/prediction-of-protein-protein-interactions
#10
Max Kotlyar, Andrea E M Rossos, Igor Jurisica
The authors provide an overview of physical protein-protein interaction prediction, covering the main strategies for predicting interactions, approaches for assessing predictions, and online resources for accessing predictions. This unit focuses on the main advancements in each of these areas over the last decade. The methods and resources that are presented here are not an exhaustive set, but characterize the current state of the field-highlighting key challenges and achievements. © 2017 by John Wiley & Sons, Inc...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902400/using-the-pride-database-and-proteomexchange-for-submitting-and-accessing-public-proteomics-datasets
#11
Andrew F Jarnuczak, Juan Antonio Vizcaíno
The ProteomeXchange (PX) Consortium is the unifying framework for world-leading mass spectrometry (MS)-based proteomics repositories. Current members include the PRIDE database (U.K.), PeptideAtlas/PASSEL, and MassIVE (U.S.A.), and jPOST (Japan). The Consortium standardizes submission and dissemination of public proteomics data worldwide. This is achieved through implementing common data submission guidelines and enforcing metadata requirements by each of the members. Furthermore, the members use a common identifier space...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902399/using-the-contextual-hub-analysis-tool-chat-in-cytoscape-to-identify-contextually-relevant-network-hubs
#12
Tanja Muetze, David J Lynn
Highly connected nodes in biological networks are called network hubs. Hubs are topologically important to the structure of the network and have been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we provide a step-by-step protocol for using the Contextual Hub Analysis Tool (CHAT), an application within Cytoscape 3, which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene or protein expression data, and identify hub nodes that are more highly connected to contextual nodes than expected by chance...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902398/using-proteomescout-a-resource-of-post-translational-modifications-their-experiments-and-the-proteins-that-they-annotate
#13
Arshag D Mooradian, Jason M Held, Kristen M Naegle
Post-translational modifications (PTMs) of protein amino acids are ubiquitous and important to protein function, localization, degradation, and more. In recent years, there has been an explosion in the discovery of PTMs as a result of improvements in PTM measurement techniques, including quantitative measurements of PTMs across multiple conditions. ProteomeScout is a repository for such discovery and quantitative experiments and provides tools for visualizing PTMs within proteins, including where they are relative to other PTMS, domains, mutations, and structure...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902397/using-sql-databases-for-sequence-similarity-searching-and-analysis
#14
William R Pearson, Aaron J Mackey
Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902396/data-analysis-pipeline-for-rna-seq-experiments-from-differential-expression-to-cryptic-splicing
#15
Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu
RNA sequencing (RNA-seq) is a high-throughput technology that provides unique insights into the transcriptome. It has a wide variety of applications in quantifying genes/isoforms and in detecting non-coding RNA, alternative splicing, and splice junctions. It is extremely important to comprehend the entire transcriptome for a thorough understanding of the cellular system. Several RNA-seq analysis pipelines have been proposed to date. However, no single analysis pipeline can capture dynamics of the entire transcriptome...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902395/finding-homologs-in-amino-acid-sequences-using-network-blast-searches
#16
Istvan Ladunga
BLAST, the Basic Local Alignment Search Tool, is used more frequently than any other biosequence database search program. We show how to run searches on the Web, and demonstrate how to increase performance by fine-tuning arguments for a specific research project. We offer guidance for interpreting results, statistical significance and biological relevance issues, and suggest complementary analyses. This unit covers both protein-to-protein (blastp) searches and translated searches (blastx, tblastn, tfastx). blastx conceptually translates the query sequence and tblastn translates all nucleotide sequences in a database, while tblastx translates both the query and the database sequences into amino acid sequences...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654729/signor-a-database-of-causal-relationships-between-biological-entities-a-short-guide-to-searching-and-browsing
#17
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
#18
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
#19
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
#20
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
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