Current Protocols in Bioinformatics 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.The HMMER Web Server for Protein Sequence Similarity Search.
Authors: Prakash A, Jeffryes M, Bateman A, Finn RD
Abstract
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 ...
Source: Current Protocols in Bioinformatics - December 10, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes.
Authors: Reiser L, Subramaniam S, Li D, Huala E
Abstract
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 ...
Source: Current Protocols in Bioinformatics - December 10, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using the Seven Bridges Cancer Genomics Cloud to Access and Analyze Petabytes of Cancer Data.
We present protocols using one of these Cloud Pilots, the Seven Bridges Cancer Genomics Cloud (CGC), to find and query public datasets, bring your own data to the CGC, analyze data using standard or custom workflows, and benchmark tools for accuracy with interactive analysis features. These protocols demonstrate that the CGC is a data-analysis ecosystem that fully empowers researchers with a variety of areas of expertise and interests to collaborate in the analysis of petabytes of data. © 2017 by John Wiley & Sons, Inc.
PMID: 29220078 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - December 10, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Finding Homologs in Amino Acid Sequences Using Network BLAST Searches.
Authors: Ladunga I
Abstract
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 ...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing.
Authors: Yalamanchili HK, Wan YW, Liu Z
Abstract
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. Here, we compile and present a robust an...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using SQL Databases for Sequence Similarity Searching and Analysis.
Authors: Pearson WR, Mackey AJ
Abstract
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. This unit d...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate.
Authors: Mooradian AD, Held JM, Naegle KM
Abstract
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 str...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs.
Authors: Muetze T, Lynn DJ
Abstract
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, integ...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.
Authors: Jarnuczak AF, Vizcaíno JA
Abstract
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. Each dataset receives a unique (PXD) ac...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Identifying Significantly Impacted Pathways and Putative Mechanisms with iPathwayGuide.
Authors: Ahsan S, Drăghici S
Abstract
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 significa...
Source: Current Protocols in Bioinformatics - June 29, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Searching Online Mendelian Inheritance in Man (OMIM): A Knowledgebase of Human Genes and Genetic Phenotypes.
Authors: Amberger JS, Hamosh A
Abstract
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. The basic protocol explains searching OMIM both fr...
Source: Current Protocols in Bioinformatics - June 29, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Exploring Short Linear Motifs Using the ELM Database and Tools.
Authors: Gouw M, Sámano-Sánchez H, Van Roey K, Diella F, Gibson TJ, Dinkel H
Abstract
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...
Source: Current Protocols in Bioinformatics - June 29, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using the NONCODE Database Resource.
Authors: Xiyuan L, Dechao B, Liang S, Yang W, Shuangsang F, Hui L, Haitao L, Chunlong L, Wenzheng F, Runsheng C, Yi Z
Abstract
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-se...
Source: Current Protocols in Bioinformatics - June 29, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Finding Similar Nucleotide Sequences Using Network BLAST Searches.
Authors: Ladunga I
Abstract
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. Understanding resul...
Source: Current Protocols in Bioinformatics - June 29, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
SIGNOR: A Database of Causal Relationships Between Biological Entities-A Short Guide to Searching and Browsing.
Authors: Lo Surdo P, Calderone A, Cesareni G, Perfetto L
Abstract
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 graphicall...
Source: Current Protocols in Bioinformatics - June 29, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
