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
    3. Cheminformatics
    4. DNA Analysis
      1. Aligning Short Sequencing Reads with Bowtie
      2. An Introduction to Sequence Similarity (“Homology”) Searching
      3. Assembling Genomic DNA Sequences with PHRAP
      4. Using CisGenome to Analyze ChIP-chip and ChIP-seq Data
      5. Finding Similar Nucleotide Sequences Using Network BLAST Searches
      6. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
      7. Generating a Genome Assembly with PCAP
      8. Genotyping in the Cloud with Crossbow
      9. An Introduction to the Informatics of “Next-Generation” Sequencing
      10. Introduction to Comparing Large Sequence Sets
      11. Using MACS to Identify Peaks from ChIP-Seq Data
      12. mtDNA Variation and Analysis Using Mitomap and Mitomaster
      13. MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences
      14. Using the NCBI Map Viewer to Browse Genomic Sequence Data
      15. Next Generation Sequence Assembly with AMOS
      16. Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools
      17. You have free access to this content
        Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome
      18. Phylogenetic Analysis with the iPlant Discovery Environment
      19. PipMaker: A World Wide Web Server for Genomic Sequence Alignments
      20. Searching NCBI's dbSNP Database
      21. Setting Up the JBrowse Genome Browser
      22. The Bluejay Genome Browser
      23. Using Apollo to Browse and Edit Genome Annotations
      24. Using Chado to Store Genome Annotation Data
      25. You have free access to this content
        Using Galaxy to Perform Large-Scale Interactive Data Analyses
      26. Using the Generic Genome Browser (GBrowse)
      27. Using the Generic Synteny Browser (GBrowse_syn)
      28. Using MEMo to Discover Mutual Exclusivity Modules in Cancer
      29. Using MUMmer to Identify Similar Regions in Large Sequence Sets
      30. Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes
      31. Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
      32. Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
      33. Using SOAPaligner for Short Reads Alignment
      34. Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
      35. Using the iPlant Collaborative Discovery Environment
      36. Using the Wash U Epigenome Browser to Examine Genome-Wide Sequencing Data
      37. Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection
      38. Using the Velvet de novo Assembler for Short-Read Sequencing Technologies
      39. Viewing and Editing Assembled Sequences Using Consed
    5. Expression Patterns
    6. Finding Genes
    7. Finding Similarities and Inferring Homologies
    8. Modeling Structure from Sequence
    9. Molecular Modeling
    10. Phylogenetic Trees
    11. Protein Analysis
    12. Proteomics
    13. Recognizing Functional Domains
    14. RNA Analysis
  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. Proteomics
  15. RNA
  16. Structural Analysis of Biomolecules
  17. Supporting Lab Techniques