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