数据库

Abstract Table of Contents Figures Literature Cited Abstract The Structure?Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web?accessible database designed to link enzyme sequence, structure, and functional information. Thi

Abstract Table of Contents Materials Figures Literature Cited Abstract Coprecipitation of proteins from whole?cell extracts is a valuable approach to testing for physical interactions between proteins of

Abstract Table of Contents Figures Literature Cited Abstract Methods for the annotation and analysis of functional sites in proteins are an area of active research, and those methods that allow detailed characterization of functional site

Abstract Table of Contents Figures Literature Cited Abstract The Dali program is widely used for carrying out automatic comparisons of protein structures determined by X?ray crystallography or NMR. The most familiar version is the Dali ser

Abstract Table of Contents Figures Literature Cited Abstract WormBase is the major public biological database for the nematode Caenorhabditis elegans. It is meant to be useful to any biologist who wants to use C. elegans, whatever his or her

Abstract Table of Contents Figures Literature Cited Abstract The PDB ligand dictionary is the chemical reference database of all the small building block molecules (e.g., amino acids, nucleic acids, and bound ligands) in the Protein Data B

Abstract Table of Contents Figures Literature Cited Abstract Neighbor Joining (NJ), FastME, and other distance?based programs including BIONJ, WEIGHBOR, and (to some extent) FITCH, are fast methods to build phylogenetic trees. This makes t

Abstract Table of Contents Literature Cited Abstract The underlying premise behind all attempts to determine a large number of diverse protein structures is that the total number of protein domain folds is much smaller, by many orders of magnitude, than the total number of

Abstract Table of Contents Figures Literature Cited Abstract One of the greatest challenges facing modern molecular biology is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requi

Abstract Table of Contents Materials Figures Literature Cited Abstract Polony DNA sequencing provides an inexpensive, accurate, high?throughput way to resequence genomes of interest by comparison to a ref

Abstract Table of Contents Figures Literature Cited Abstract Microarray experiments require careful planning and choice of analysis tools in order to get the most out of the data generated, especially considering the associated significant

Abstract Table of Contents Materials Figures Literature Cited Abstract BLAST is a widely used genetic sequence comparison program developed at the National Center for Biotechnology Information (NCBI). In

Abstract Table of Contents Figures Literature Cited Abstract This appendix discusses a few of the file formats frequently encountered in bioinformatics. Specifically, it reviews the rules for generating FASTA files and provides guidance fo

Abstract Table of Contents Figures Literature Cited Abstract DTASelect provides a means by which complex SEQUEST results can be filtered, organized, and viewed. A single sample may produce tens of thousands of tandem mass spectra. Manually

Abstract Table of Contents Figures Literature Cited Abstract Electrostatic free energy is useful for correlating structure with function in proteins in which ionizable groups play essential functional roles. To this end, the pKa values of

Abstract Table of Contents Figures Literature Cited Abstract Logging in to a Unix system from a console typically initiates a graphical desktop environment that is similar to the Microsoft Windows and Apple Macintosh desktops. Logging in r

Abstract Table of Contents Figures Literature Cited Abstract The PHRAP assembly program provides rapid comparison, alignment, and assembly of large sets of DNA sequences. PHRAP compares sequences by searching for pairs of perfectly matchin

Abstract Table of Contents Figures Literature Cited Abstract CMap is a Web?based tool for viewing comparisons between biological maps of different types. It allows for correspondences to be displayed between maps as disparate as genetic an

Abstract Table of Contents Literature Cited Abstract After providing a brief introduction to microarray chips and experimental details, this overview discusses analysis techniques. Data analysis from microarray experiments generally involves two parts: acquiring and no ...

Abstract Table of Contents Figures Literature Cited Abstract The Minimotif Miner Web site contains information on several hundred short functional motifs in a single database, and allows the user to search protein queries for the presence