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
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        BEDTools: The Swiss-Army Tool for Genome Feature Analysis
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        cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing
      6. Using CisGenome to Analyze ChIP-chip and ChIP-seq Data
      7. DNA Motif Databases and Their Uses
      8. Efficient Alignment of Illumina-Like High-Throughput Sequencing Reads with the GEnomic Multi-tool (GEM) Mapper
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        Finding Protein and Nucleotide Similarities with FASTA
      10. Finding Similar Nucleotide Sequences Using Network BLAST Searches
      11. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
      12. Generating a Genome Assembly with PCAP
      13. Genome Annotation and Curation Using MAKER and MAKER-P
      14. Genotyping in the Cloud with Crossbow
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        Inference of Episodic Changes in Natural Selection Acting on Protein Coding Sequences via CODEML
      16. An Introduction to the Informatics of “Next-Generation” Sequencing
      17. Introduction to Comparing Large Sequence Sets
      18. Using MACS to Identify Peaks from ChIP-Seq Data
      19. mtDNA Variation and Analysis Using Mitomap and Mitomaster
      20. MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences
      21. Using the NCBI Map Viewer to Browse Genomic Sequence Data
      22. Next Generation Sequence Assembly with AMOS
      23. Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools
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        Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome
      25. Phylogenetic Analysis with the iPlant Discovery Environment
      26. PipMaker: A World Wide Web Server for Genomic Sequence Alignments
      27. Searching NCBI's dbSNP Database
      28. Setting Up the JBrowse Genome Browser
      29. The Bluejay Genome Browser
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        The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses
      31. Using Apollo to Browse and Edit Genome Annotations
      32. Using Chado to Store Genome Annotation Data
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        Using Galaxy to Perform Large-Scale Interactive Data Analyses
      34. Using the Generic Genome Browser (GBrowse)
      35. Using the Generic Synteny Browser (GBrowse_syn)
      36. Using MEMo to Discover Mutual Exclusivity Modules in Cancer
      37. Using MUMmer to Identify Similar Regions in Large Sequence Sets
      38. Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes
      39. Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
      40. Using RAxML to Infer Phylogenies
      41. Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
      42. Using SOAPaligner for Short Reads Alignment
      43. Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
      44. Using the iPlant Collaborative Discovery Environment
      45. Using the Wash U Epigenome Browser to Examine Genome-Wide Sequencing Data
      46. Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection
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        VAGrENT: Variation Annotation Generator
      48. Using the Velvet de novo Assembler for Short-Read Sequencing Technologies
      49. Viewing and Editing Assembled Sequences Using Consed
    5. Expression Patterns
    6. Finding Genes
    7. Finding Similarities and Inferring Homologies
    8. Genome Variation
    9. Modeling Structure from Sequence
    10. Molecular Modeling
    11. Pathways and Molecular Interactions
    12. Phylogenetic Trees
    13. Protein Analysis
    14. Proteomics
    15. Recognizing Functional Domains
    16. RNA Analysis
    17. 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

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