数据库

Abstract Table of Contents Figures Literature Cited Abstract Comparison of DNA sequences from different species is a fundamental method for identifying functional elements, such as exons or enhancers, as they tend to exhibit significant se

Abstract Table of Contents Figures Literature Cited Abstract The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user?friendliness. Beginner and intermediate users will learn how to desi

Abstract Table of Contents Figures Literature Cited Abstract In the past fifteen years, new classes of regulatory RNAs have been discovered, previously hidden in the transcriptome mostly due to their small size. These small regulatory RNAs

Abstract Table of Contents Figures Literature Cited Abstract High?throughput genomics screening studies, such as microarray, proteomics, etc., often result in large, ?interesting? gene lists, ranging in size from hundreds to thousands of g

Abstract Table of Contents Figures Literature Cited Abstract Transcription profiling with microarrays has become a standard procedure for comparing the levels of gene expression between pairs of samples, or multiple samples following diffe

Abstract Table of Contents Figures Literature Cited Abstract Synteny blocks are composed of two or more orthologous genes conserved among species, resulting from speciation from their last common ancestor. OrthoCluster (Zeng et al., 2008)

Abstract Table of Contents Figures Literature Cited Abstract Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome

Abstract Table of Contents Materials Figures Literature Cited Abstract The protocol in this unit describes the steps for gene expression analysis of Haemophilus influenzae in broth culture. Steps for hot ac

Abstract Table of Contents Figures Literature Cited Abstract Sage?N's Sorcerer 2 provides an integrated data analysis system for comprehensive protein identification and characterization. It runs on a proprietary version of SEQUESTR, the m

Abstract Table of Contents Figures Literature Cited Abstract A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. T

Abstract Table of Contents Materials Figures Literature Cited Abstract High?throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require

Abstract Table of Contents Materials Figures Literature Cited Abstract A recently developed technique called RNA Sequencing (RNA?Seq) uses massively parallel sequencing to allow transcriptome analyses of

Abstract Table of Contents Figures Literature Cited Abstract There are many structures that can be adopted by nucleic acids other than the Watson?Crick duplex. In particular, a noncanonical four?stranded topology, called a G?quadruplex, is

Abstract Table of Contents Figures Literature Cited Abstract Quantitative analysis has become increasingly important in the proteomics field; however, the large amount of mass spectrometric data and the different types of quantitative stra

Abstract Table of Contents Figures Literature Cited Abstract miRBase is the central repository for microRNA (miRNA) sequence information. miRBase has a role in defining the nomenclature for miRNA genes and assigning names to novel miRNAs f

Abstract Table of Contents Figures Literature Cited Abstract In this unit, we describe assembly of a multiple sequence alignment using the T?Coffee package. T?Coffee is much more flexible than most related methods (e.g., ClustalW) because

Abstract Table of Contents Figures Literature Cited Abstract The DFCI Gene Index Web pages provide access to analyses of ESTs and gene sequences for nearly 114 species, as well as a number of resources derived from these. Each species?spec

Abstract Table of Contents Figures Literature Cited Abstract Spectral library searching is an emerging approach in proteomic data analysis for the inference of peptide identifications from tandem mass spectra. It offers a promising alterna

Abstract Table of Contents Figures Literature Cited Abstract The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories designed to store, disseminate, and analyze mass spectrometry?based prot

Abstract Table of Contents Figures Literature Cited Abstract Depositing data to a public domain interaction database not only improves the quality and quantity of interactions available to the user community, but also increases the visibil