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Applied Bioinformatics
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Applied Bioinformatics

Tác giả: David A. Hendrix

Nhà xuất bản: Project Gutenberg

Thể loại: Y học sức khỏe

Định dạng: Epub

Lượt xem: 6389

Ngày cập nhật: 14/04/2021

Đọc ebook

Thông tin chi tiết

Book Description: The current edition of the book may be downloaded from the Applied Bioinformatics site.

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  1. Applied Bioinformatics

    1. Applied Bioinformatics

  2. Foreword

    1. Foreword

  3. Dedication

    1. For the students and learners of the world.

    1. Chapter 1: Introduction to Biological Sequences, Biopython, and GNU/Linux

      1. 1.1 Nucleic Acid Bioinformatics
      2. 1.2 Sequences, Strings, and the Genetic Code
      3. 1.3 Sequences File Formats
      4. 1.4 Lab 1: Introduction to GNU/Linux and Fasta files
      5. 1.5 Biological Sequence Database
      6. 1.6 Lab 2: FASTQ and Quality Scores

    2. Chapter 2: Sequence Motifs

      1. 2.1 Introduction to Motifs
      2. 2.2 String Matching
      3. 2.3 Consensus Sequences
      4. 2.4 Motif Finding
      5. 2.5 Promoters
      6. 2.6 De novo Motif Finding
      7. 2.7 Lab 3: Introduction to Motifs

    3. Chapter 3: Sequence Alignments

      1. 3.1 Alignment Algorithms and Dynamic Programming
      2. 3.2 Alignment Software
      3. 3.3 Alignment Statistics
      4. 3.4 Short Read Mapping
      5. 3.5 Lab 4: Using BLAST on the command line

    4. Chapter 4: Multiple Sequence Alignments, Molecular Evolution, and Phylogenetics

      1. 4.1 Multiple Sequence Alignment
      2. 4.2 Phylogenetic Trees
      3. 4.3 Models of mutations
      4. 4.4 Lab 5: Phylogenetics

    5. Chapter 5: Genomics

      1. 5.1 The Three Fundamental “Gotchas” of Genomics
      2. 5.2 Genomic Data and File Formats
      3. 5.3 Genome Browsers
      4. 5.4 Lab 6: Genome Annotation Data

    6. Chapter 6: Transcriptomics

      1. 6.1 High-throughout Sequencing (HTS)
      2. 6.2 RNA Deep Sequencing
      3. 6.3 Small RNA sequencing
      4. 6.4 Long RNA sequencing
      5. 6.5 Single-Cell Transcriptomics
      6. 6.6 Transcription Initiation
      7. 6.7 Transcription
      8. 6.8 Elongation
      9. 6.9 Lab 7: RNA-seq

    7. Chapter 7: Noncoding RNAs

      1. 7.1 Small Noncoding RNAs (srcRNAs)
      2. 7.2. Long Noncoding RNAs
      3. 7.3 RNA Structure Prediction
      4. 7.4 Destabilizing energies
      5. 7.5 Lab 8: RNA Structure

    8. Chapter 8: Proteins

      1. 8.1 Protein Alignment
      2. 8.2 Functional Annotation of Proteins
      3. 8.3 Secondary Structure prediction
      4. 8.4 Gene Ontology
      5. 8.5 Lab 9: Proteins

    9. Chapter 9: Gene Regulation

      1. 9.1 Transcription Factors and ChIP-seq
      2. 9.2 MicroRNA regulation and Small RNA-seq
      3. 9.3 Regulatory Networks
      4. 9.4 Lab 10: ChIP-seq

  5. Appendix A: Mathematical Preliminaries

  6. Appendix B: Probability

  7. Bibliography

  8. Creative Commons License

  9. Recommended Citations

  10. Versioning

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