Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Online ISBN: 9780471250951

DOI: 10.1002/0471250953

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  1. Bioinformatics
  2. Bioinformatics
    1. Bioinformatics Fundamentals
    2. Biological Databases
      1. Access Guide to Human Proteinpedia
      2. Administering GBrowse Sites with WebGBrowse
      3. Creating Databases for Biological Information: An Introduction
      4. Using the DFCI Gene Index Databases for Biological Discovery
      5. DIANA-TarBase and DIANA Suite Tools: Studying Experimentally Supported microRNA Targets
      6. DNA Motif Databases and Their Uses
      7. You have free access to this content
        Exploring FlyBase Data Using QuickSearch
      8. Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database
      9. Exploring Zebrafish Genomic, Functional and Phenotypic Data Using ZFIN
      10. Extracting Biological Meaning from Large Gene Lists with DAVID
      11. Human Mutation Databases
      12. Identifying Functional Sites Based on Prediction of Charged Group Behavior
      13. Installing a Local Copy of the Reactome Web Site and Knowledgebase
      14. Installing and Configuring CMap
      15. Investigating Protein Structure and Evolution with SCOP2
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        MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases
      17. MetaboLights: An Open-Access Database Repository for Metabolomics Data
      18. Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities
      19. miRBase: microRNA Sequences and Annotation
      20. Modeling Biology Using Relational Databases
      21. mtDNA Variation and Analysis Using Mitomap and Mitomaster
      22. Using the NCBI Map Viewer to Browse Genomic Sequence Data
      23. PharmGKB: An Integrated Resource of Pharmacogenomic Data and Knowledge
      24. PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature
      25. Searching and Navigating UniProt Databases
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        Searching NCBI Databases Using Entrez
      27. Searching NCBI's dbSNP Database
      28. Searching Online Mendelian Inheritance in Man (OMIM) for Information on Genetic Loci Involved in Human Disease
      29. Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype
      30. Searching WormBase for Information about Caenorhabditis elegans
      31. Setting Up the JBrowse Genome Browser
      32. Structured Query Language (SQL) Fundamentals
      33. Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND)
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        The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses
      35. The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution
      36. The Importance of Biological Databases in Biological Discovery
      37. The UCSC Genome Browser
      38. Using Apollo to Browse and Edit Genome Annotations
      39. Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins
      40. Using Chado to Store Genome Annotation Data
      41. Using DrugBank for In Silico Drug Exploration and Discovery
      42. Using EMBL-EBI Services via Web Interface and Programmatically via Web Services
      43. Using the Ensembl Genome Server to Browse Genomic Sequence Data
      44. Using the Generic Genome Browser (GBrowse)
      45. Using the Generic Synteny Browser (GBrowse_syn)
      46. Using the MetaCyc Pathway Database and the BioCyc Database Collection
      47. Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
      48. Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
      49. Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds
      50. Using the iPlant Collaborative Discovery Environment
      51. Using the KEGG Database Resource
      52. Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates
      53. Using the Reactome Database
      54. Using the Saccharomyces Genome Database (SGD) for Analysis of Genomic Information
      55. Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes
      56. Using the Tools and Resources of the RCSB Protein Data Bank
      57. Using the Tools and Resources of the RCSB Protein Data Bank
    3. Cheminformatics
    4. DNA Analysis
    5. Expression Patterns
    6. Finding Genes
    7. Finding Similarities and Inferring Homologies
    8. Genome Variation
    9. Metabolomics
    10. Modeling Structure from Sequence
    11. Molecular Modeling
    12. Pathways and Molecular Interactions
    13. Phylogenetic Trees
    14. Protein Analysis
    15. Proteomics
    16. Recognizing Functional Domains
    17. RNA Analysis
    18. Sequence Mapping and Assembly
  3. Cell Biology
  4. Chemical Biology
  5. Gene Expression
  6. Genetics and Genomics
  7. Genetics and Genomics
  8. Intermolecular Interactions
  9. Intermolecular Interactions
  10. Microbiology
  11. Molecular Biology
  12. Nucleic Acid Chemistry
  13. Pharmacology and Drug Discovery
  14. Protein Production, Purification, and Analysis
  15. Proteomics
  16. RNA
  17. Structural Analysis of Biomolecules
  18. Supporting Lab Techniques