Steve Jupe,Antonio Fabregat,Henning Hermjakob
Steve Jupe
The Reactome database of curated biological pathways provides a tool for visualizing user-supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the path...
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST [0.03%]
用MiST打分大规模亲和纯化质谱数据集
Erik Verschueren,John Von Dollen,Peter Cimermancic et al.
Erik Verschueren et al.
High-throughput Affinity Purification Mass Spectrometry (AP-MS) experiments can identify a large number of protein interactions, but only a fraction of these interactions are biologically relevant. Here, we describe a comprehensive computat...
Ernesto Picardi,Anna Maria D&#x;Erchia,Antonio Montalvo et al.
Ernesto Picardi et al.
RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organ...
Antonina Andreeva,Dave Howorth,Cyrus Chothia et al.
Antonina Andreeva et al.
SCOP2 is a successor to the Structural Classification of Proteins (SCOP) database that organizes proteins of known structure according to their structural and evolutionary relationships. It was designed to provide a more advanced framework ...
PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra [0.03%]
PepArML：一种元搜索多肽鉴定平台用于串联质谱数据
Nathan J Edwards
Nathan J Edwards
The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised...
Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection [0.03%]
使用VarScan 2进行基因组变异识别和体细胞突变检测
Daniel C Koboldt,David E Larson,Richard K Wilson
Daniel C Koboldt
The identification of small sequence variants remains a challenging but critical step in the analysis of next-generation sequencing data. Our variant calling tool, VarScan 2, employs heuristic and statistic thresholds based on user-defined ...
DXMSMS Match Program for Automated Analysis of LC-MS/MS Data Obtained Using Isotopically Coded CID-Cleavable Cross-Linking Reagents [0.03%]
基于同位素标记的裂解型交联剂获得的LC-MS/MS数据的自动化分析中的DXMSMS匹配程序
Evgeniy V Petrotchenko,Karl A T Makepeace,Christoph H Borchers
Evgeniy V Petrotchenko
Cross-linking combined with mass spectrometry for the study of proteins and protein complexes is greatly facilitated by the use of isotopically coded cleavable cross-linking reagents. The isotopic coding of the cross-linker enables confiden...
Michael S Campbell,Carson Holt,Barry Moore et al.
Michael S Campbell et al.
This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein-coding and noncoding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality...
Clustal omega [0.03%]
Clustal Omega
Fabian Sievers,Desmond G Higgins
Fabian Sievers
Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega...
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services [0.03%]
EMBL-EBI数据库的网页界面和网络服务的程序使用方法
Rodrigo Lopez,Andrew Cowley,Weizhong Li et al.
Rodrigo Lopez et al.
The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are availabl...