数据库

Abstract Table of Contents Figures Literature Cited Abstract This unit introduces the concept of hidden Markov models in computational biology. It describes them using simple biological examples, requiring as little mathematical knowledge

Abstract Table of Contents Figures Literature Cited Abstract DrugBank is a fully curated drug and drug target database that contains information on nearly 5000 drugs, including 1200 FDA?approved small molecule and biotech drugs as well as

Abstract Table of Contents Literature Cited Abstract Cheminformatics is a relatively new field of information technology that focuses on the collection, storage, analysis, and manipulation of chemical data. The chemical data of interest typically includes information on sma

Abstract Table of Contents Figures Literature Cited Abstract This unit describes the usage of geneid, an efficient gene?finding program that allows for the analysis of large genomic sequences, including whole mammalian chromosomes. These s

Abstract Table of Contents Figures Literature Cited Abstract Mass spectrometry?based methods for the identification of proteins are fundamental platform technologies for proteomics. One comprehensive approach is to subject trypsinized pept

Abstract Table of Contents Figures Literature Cited Abstract ProSight PTM v2.0, neuroProSight, and the Sequence Gazer allow the identification and characterization of proteins from high mass accuracy tandem mass spectrometric data of intac

Abstract Table of Contents Figures Literature Cited Abstract The functions of many noncoding RNAs and cis?acting regulatory elements of mRNAs depend on a defined RNA secondary structure. RNAz predicts such functional RNA structures on the

Abstract Table of Contents Figures Literature Cited Abstract Understanding gene regulation has been and remains one of the major challenges for the molecular biology community. Gene regulation is mediated by a variety of short DNA sequence

Abstract Table of Contents Figures Literature Cited Abstract Computational biology/chemistry tools are used in most areas of life/health science research. These methods are continually being developed and their use can present difficulties

Abstract Table of Contents Figures Literature Cited Abstract Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an accurate three?dimensional (3?D) structure of the studied p

Abstract Table of Contents Figures Literature Cited Abstract BiblioSpec is a software package for creating and searching libraries of tandem MS peptide spectra. Library searching provides a quick method for making peptide?spectrum matches

Abstract Table of Contents Figures Literature Cited Abstract The MetaCyc database (http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual cur

Abstract Table of Contents Figures Literature Cited Abstract The iHOP (Information Hyperlinked over Proteins) resource employs sophisticated text?mining methods to assist researchers in their quest for information on specific genes and pro

Abstract Table of Contents Figures Literature Cited Abstract New mutation detection technologies must keep pace by becoming more cost?effective while offering improved technical sensitivity and higher throughput capacity. In recent years,

Abstract Table of Contents Figures Literature Cited Abstract Genome?based peptide fingerprint scanning (GFS) directly maps several types of protein mass spectral (MS) data to the loci in the genome that may have encoded for the protein. Th

Abstract Table of Contents Figures Literature Cited Abstract The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE dat

Abstract Table of Contents Figures Literature Cited Abstract The Reactome project builds, maintains, and publishes a database of biological pathways. The information in the database is gathered from the experts in the field, peer reviewed,

Abstract Table of Contents Materials Figures Literature Cited Abstract Bisulfite is known to deaminate cytosine in nucleic acids, while 5?methylcytosine resists this bisulfite action. For this reason, bis

Abstract Table of Contents Figures Literature Cited Abstract The ZINC database of commercially available compounds contains biologically relevant representations of purchasable compounds in ready?to?screen formats. ZINC uses catalogs from

Abstract Table of Contents Figures Literature Cited Abstract ChemBank (http://chembank.broad.harvard.edu/) is a public, Web?based informatics environment. ChemBank stores and makes freely available data derived from small molecules and sma