Current Protocols in Bioinformatics

Copyright © 1999-2012 by John Wiley and Sons, Inc. All Rights Reserved.

Current Protocols in Bioinformatics

Online ISBN: 9780471250951

DOI: 10.1002/0471250953

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  1. Bioinformatics
  2. Bioinformatics
    1.  
    2. Bioinformatics Fundamentals
    3. Biological Databases
    4. Cheminformatics
    5. DNA Analysis
    6. Expression Patterns
    7. Finding Genes
    8. Finding Similarities and Inferring Homologies
      1. Aligning Short Sequencing Reads with Bowtie
      2. An Introduction to Sequence Similarity (“Homology”) Searching
      3. An Overview of Multiple Sequence Alignment
      4. Clustal Omega
      5. Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite
      6. Using the DFCI Gene Index Databases for Biological Discovery
      7. FAMS and FAMSBASE for Protein Structure
      8. Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
      9. Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program
      10. Finding Protein and Nucleotide Similarities with FASTA
      11. Finding Similar Nucleotide Sequences Using Network BLAST Searches
      12. Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P-POD)
      13. Installing and Configuring CMap
      14. Installing, Maintaining, and Using a Local Copy of BLAST for Intranet and Workstation Use
      15. Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch
      16. Identification of Novel and Known miRNAs in Deep-Sequencing Data with miRDeep2
      17. MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences
      18. Computing Multiple Sequence/Structure Alignments with the T-Coffee Package
      19. Next Generation Sequence Assembly with AMOS
      20. Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools
      21. Protein Function Prediction: Problems and Pitfalls
      22. Searching NCBI's dbSNP Database
      23. Selecting the Right Similarity-Scoring Matrix
      24. Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families
      25. Using BLAT to Find Sequence Similarity in Closely Related Genomes
      26. Using Dali for Structural Comparison of Proteins
      27. Using the Generic Synteny Browser (GBrowse_syn)
      28. You have free access to this content
        Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New Ortholog Groups
      29. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
    9. Genome Variation
    10. Metabolomics
    11. Modeling Structure from Sequence
    12. Molecular Modeling
    13. Pathways and Molecular Interactions
    14. Phylogenetic Analysis
    15. Protein Analysis
    16. Proteomics
    17. Recognizing Functional Domains
    18. RNA Analysis
    19. 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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