Gary D Stormo
Gary D Stormo
This unit provides an overview of issues involved in domain recognition in protein and DNA sequences. It opens with a discussion of the two primary methods of domain representation, namely consensus sequences and alignment matrices (e.g., t...
Metabolomic data processing, analysis, and interpretation using MetaboAnalyst [0.03%]
利用代谢分析家（MetaboAnalyst）处理、分析和解释代谢组数据
Jianguo Xia,David S Wishart
Jianguo Xia
MetaboAnalyst is a comprehensive, Web-based tool designed for processing, analyzing, and interpreting metabolomic data. It handles most of the common metabolomic data types including compound concentration lists, spectral bin lists, peak li...
Gretchen Gibney,Andreas D Baxevanis
Gretchen Gibney
One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries fo...
Andreas D Baxevanis
Andreas D Baxevanis
Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit...
Ram Podicheti,Qunfeng Dong
Ram Podicheti
GBrowse is widely used by biologists to visualize genome annotation. We have developed WebGBrowse to facilitate hosting multiple GBrowse instances specific for different users on the same Web server. WebGBrowse automatically sets up each us...
Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD) [0.03%]
基于普林斯顿蛋白质同源性数据库(P-POD)的从同源性推理蛋白功能的方法
Michael S Livstone,Rose Oughtred,Sven Heinicke et al.
Michael S Livstone et al.
Inferring a protein's function by homology is a powerful tool for biologists. The Princeton Protein Orthology Database (P-POD) offers a simple way to visualize and analyze the relationships between homologous proteins in order to infer func...
Hongkai Ji,Hui Jiang,Wenxiu Ma et al.
Hongkai Ji et al.
Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are high-throughput approaches to profiling genome-wide protein-DNA interactions. ...
Todd J Treangen,Dan D Sommer,Florent E Angly et al.
Todd J Treangen et al.
A Modular Open-Source Assembler (AMOS) was designed to offer a modular approach to genome assembly. AMOS includes a wide range of tools for assembly, including the lightweight de novo assemblers Minimus and Minimo, and Bambus 2, a robust sc...
Mitchell E Skinner,Ian H Holmes
Mitchell E Skinner
JBrowse is a Web-based tool for visualizing genomic data. Unlike most other Web-base genome browsers, JBrowse exploits the capabilities of the user's Web browser to make scrolling and zooming fast and smooth. It supports the browsers used b...
Ben Langmead
Ben Langmead
This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bow...