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.BreakDancer - Identification of Genomic Structural Variation from Paired-End Read Mapping.
Authors: Fan X, Abbott TE, Larson D, Chen K
Abstract
The advent of the next-generation sequencing data has made it possible to cost-effectively detect and characterize genomic variation in human genomes. Structural variation, including deletion, duplication, insertion, inversion and translocation, is of great importance to human genetics due to its association with many genetic diseases. BreakDancer is a bioinformatics tool that relates paired-end read alignments from a test genome to the reference genome for the purpose of comprehensively and accurately detecting various types of structural variation.
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Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases.
Authors: Rappaport N, Twik M, Nativ N, Stelzer G, Bahir I, Stein TI, Safran M, Lancet D
Abstract
Systems medicine provides insights into mechanisms of human diseases, and expedites the development of better diagnostics and drugs. To facilitate such strategies, we initiated MalaCards, a compendium of human diseases and their annotations, integrating and often remodeling information from 64 data sources. MalaCards employs, among others, the proven automatic data-mining strategies established in the construction of GeneCards, our widely used compendium of human genes. The development of MalaCards poses many a...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
BEDTools: The Swiss-Army Tool for Genome Feature Analysis.
Authors: Quinlan AR
Abstract
Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi-dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high-throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools oper...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences.
Authors: Zambelli F, Pesole G, Pavesi G
Abstract
One of the greatest challenges facing modern molecular biology is understanding the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of sequence motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors (TFs) with their corresponding binding sites. Weeder, Pscan, and PscanChIP are software tools freely available for noncommercial users as a stand-alone or Web-based ...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Comparative Protein Structure Modeling Using MODELLER.
Authors: Webb B, Sali A
Abstract
Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). T...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Biological network exploration with cytoscape 3.
Authors: Su G, Morris JH, Demchak B, Bader GD
Abstract
Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of ...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
