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SCOP: a structural classification of proteins database for the investigation of sequences and structures.
This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure and provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Expand
WebLogo: a sequence logo generator.
WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarityExpand
The Bioperl toolkit: Perl modules for the life sciences.
The overall architecture of the Bioperl toolkit is described, the problem domains that it addresses, and specific examples of how the toolkit can be used to solve common life-sciences problems are given. Expand
Data growth and its impact on the SCOP database: new developments
Pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships, is introduced and the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies is discussed. Expand
SCOP database in 2004: refinements integrate structure and sequence family data
A refinement of the SCOP classification is initiated, which introduces a number of changes mostly at the levels below superfamily, and modernization of the interface capabilities of SCOP allowing more dynamic links with other databases is started. Expand
The Transcriptional Landscape of the Mammalian Genome
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. Expand
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans
It is proposed that regulated unproductive splice and translation (RUST), through the coupling of alternative splicing and NMD, may be a pervasive, underappreciated means of regulating protein expression. Expand
The ASTRAL compendium for protein structure and sequence analysis
The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences, and summarizes the overall characteristics of a protein structure. Expand
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Two studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Expand
SCOP: a Structural Classification of Proteins database
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is onExpand