数据库

Abstract Table of Contents Figures Literature Cited Abstract N?Browse is a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data. N?Browse runs as a Java applet in a Web browser, providi

Abstract Table of Contents Figures Literature Cited Abstract Cytoscape is a free software package for visualizing, modeling, and analyzing molecular and genetic interaction networks. As a key feature, Cytoscape enables biologists to determ

Abstract Table of Contents Figures Literature Cited Abstract ArrayExpress at the European Bioinformatics Institute is a public database for MIAME?compliant microarray and transcriptomics data. It consists of two parts: the ArrayExpress Rep

Abstract Table of Contents Materials Figures Literature Cited Abstract The ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the avail

Abstract Table of Contents Figures Literature Cited Abstract This unit describes how to set up and analyze ligand?protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring funct

Abstract Table of Contents Figures Literature Cited Abstract VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.

Abstract Table of Contents Figures Literature Cited Abstract The Human Metabolome Database (HMDB) is a Web?based bioinformatic/cheminformatic resource with detailed information about human metabolites and metabolic enzymes. It can be used

Abstract Table of Contents Figures Literature Cited Abstract De novo sequencing is an effective method for identifying unknown peptide sequences from their tandem mass spectra. This unit briefly introduces how this can be done manually. A

Abstract Table of Contents Figures Literature Cited Abstract RepeatMasker is a popular software tool widely used in computational genomics to identify, classify, and mask repetitive elements, including low?complexity sequences and interspe

Abstract Table of Contents Figures Literature Cited Abstract The Basic Local Alignment Search Tool (BLAST) is the most fundamental (and most misused) algorithm and software in bioinformatics/computational biology for functional assessment

Abstract Table of Contents Figures Literature Cited Abstract The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data i

Abstract Table of Contents Figures Literature Cited Abstract Protein sequence comparison and search has become commonplace not only for bioinformatics researchers but also for experimentalists in many cases. Because of the exponential grow

Abstract Table of Contents Materials Figures Literature Cited Abstract PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main fun

Abstract Table of Contents Figures Literature Cited Abstract Model Organism Databases (MODs) represent the union of database technology and biology, and are essential to modern biological and medical research. Research communities are prod

Abstract Table of Contents Figures Literature Cited Abstract Phylogenetic trees represent hypotheses about evolutionary relationships between organisms or nucleotide or amino acid sequences. Because the best BLAST hit often does not repres

Abstract Table of Contents Materials Figures Literature Cited Abstract In the post?genomic era, more and more research projects involve the generation of molecular sequence data. How should these newly ob

Abstract Table of Contents Figures Literature Cited Abstract BLAST is the most widely used software in bioinformatics research. Its main function is to compare a sequence of interest, the query sequence, to sequences in a large database. B

Abstract Table of Contents Figures Literature Cited Abstract Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ?small? chemical compounds. This unit provides a detailed guide

Abstract Table of Contents Figures Literature Cited Abstract This unit shows how to use the RNAshapes package for the prediction of the secondary structure of a single RNA sequence using either minimum free energy methods or weighted ensem

Abstract Table of Contents Figures Literature Cited Abstract This unit documents how to use the Vienna RNA package for RNA secondary structure analysis. Possible tasks include structure prediction for single sequences, prediction of consen