Good Citizenship Made Easy: A Step-by-Step Guide to Submitting RNA-Seq Data to NCBI [0.03%]
轻松成为一名优秀公民：提交转录组数据至NCBI的步步指南
Wiebke Feindt,Sara J Oppenheim,Robert DeSalle et al.
Wiebke Feindt et al.
The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is...
Yanyan Ju,Jing Gong,Yucheng T Yang et al.
Yanyan Ju et al.
RNA-RNA interactions (RRIs) are essential to understanding the regulatory mechanisms of RNAs. Mapping RRIs in vivo in a transcriptome-wide manner remained challenging until the recent development of several sequencing-based technologies. Ho...
Tyler Alioto,Enrique Blanco,Genís Parra et al.
Tyler Alioto et al.
This unit describes the usage of geneid, an efficient gene-finding program that allows for the analysis of large genomic sequences, including whole mammalian chromosomes. These sequences can be partially annotated, and geneid can be used to...
Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use [0.03%]
计算集群或工作站中BLAST的本地拷贝的安装维护及使用方法
Istvan Ladunga
Istvan Ladunga
The Basic Local Alignment Search Tool (BLAST) is the first resource to computationally characterize a novel amino acid or nucleic acid sequence. BLAST plays important roles in genomics, transcriptomics, and protein science. For numerous aca...
Analysis and Visualization of Dynamic Networks Using the DyNet App for Cytoscape [0.03%]
用于Cytoscape的DyNet应用程序的动态网络分析和可视化
John Salamon,Ivan H Goenawan,David J Lynn
John Salamon
Biological processes are regulated at a cellular level by tightly controlled molecular interaction networks, which are collectively known as the interactome. The interactome is not a static entity, but instead is dynamically reorganized or ...
Kapeel M Chougule,Liya Wang,Joshua C Stein et al.
Kapeel M Chougule et al.
RNA-seq is a vital method for understanding gene structure and expression patterns. Typical RNA-seq analysis protocols use sequencing reads of length 50 to 150 nucleotides for alignment to the reference genome and assembly of transcripts. T...
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome [0.03%]
利用实验细节以期更深入地了解宿主病原微生物交互组学中的相互作用
Mais Ammari,Fiona McCarthy,Bindu Nanduri
Mais Ammari
An increasing proportion of curated host-pathogen interaction (HPI) information is becoming available in interaction databases. These data represent detailed, experimentally-verified, molecular interaction data, which may be used to better ...
Accessing Expert-Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY [0.03%]
IUPHAR/BPS 药物指南中的专家药理学数据及其获取方式
Joanna L Sharman,Simon D Harding,Christopher Southan et al.
Joanna L Sharman et al.
The IUPHAR/BPS Guide to PHARMACOLOGY is an expert-curated, open-access database of information on drug targets and the substances that act on them. This unit describes the procedures for searching and downloading ligand-target binding data ...
R Dustin Schaeffer,Yuxing Liao,Nick V Grishin
R Dustin Schaeffer
ECOD is a database of evolutionary domains from structures deposited in the PDB. Domains in ECOD are classified by a mixed manual/automatic method wherein the bulk of newly deposited structures are classified automatically by protein-protei...
Exploring Biological Networks in 3D, Stereoscopic 3D, and Immersive 3D with iCAVE [0.03%]
利用iCAVE探索三维（立体三维和沉浸式三维）生物网络
Selim Kalayci,Zeynep H Gümüş
Selim Kalayci
Biological networks are becoming increasingly large and complex, pushing the limits of existing 2D tools. iCAVE is an open-source software tool for interactive visual explorations of large and complex networks in 3D, stereoscopic 3D, or imm...