Ananth Prakash,Matt Jeffryes,Alex Bateman et al.
Ananth Prakash et al.
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-...
Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER [0.03%]
基于3D-SURFER2.0和EM-SURFER的蛋白质三维结构及电子显微重构图谱检索
Xusi Han,Qing Wei,Daisuke Kihara
Xusi Han
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...
Max Kotlyar,Andrea E M Rossos,Igor Jurisica
Max Kotlyar
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 fo...
Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets [0.03%]
利用PRIDE数据库和ProteomeXchange提交和访问公共蛋白质组学数据集
Andrew F Jarnuczak,Juan Antonio Vizcaíno
Andrew F Jarnuczak
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 (J...
Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs [0.03%]
利用Cytoscape中的上下文中心工具（CHAT）识别相关的网络中枢
Tanja Muetze,David J Lynn
Tanja Muetze
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...
Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate [0.03%]
使用ProteomeScout：一个包含蛋白质修饰、实验和注释蛋白的资源
Arshag D Mooradian,Jason M Held,Kristen M Naegle
Arshag D Mooradian
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 impro...
William R Pearson,Aaron J Mackey
William R Pearson
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 th...
Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing [0.03%]
RNA测序实验的数据分析流程：从差异表达到隐蔽剪接
Hari Krishna Yalamanchili,Ying-Wooi Wan,Zhandong Liu
Hari Krishna Yalamanchili
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 sp...
Finding Homologs in Amino Acid Sequences Using Network BLAST Searches [0.03%]
基于网络的BLAST搜索在氨基酸序列中寻找同系物
Istvan Ladunga
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 spe...
SIGNOR: A Database of Causal Relationships Between Biological Entities-A Short Guide to Searching and Browsing [0.03%]
SIGNOR：生物实体之间因果关系的数据库-搜索和浏览简明指南
Prisca Lo Surdo,Alberto Calderone,Gianni Cesareni et al.
Prisca Lo Surdo et al.
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-reg...