Computer Manipulation of DNA and Protein Sequences

J. Michael Cherry1

1 Stanford University, Palo Alto, California
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 7.7
DOI:  10.1002/0471142727.mb0707s30
Online Posting Date:  May, 2001
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Abstract

This unit outlines a variety of methods by which DNA sequences can be manipulated by computers. Procedures for entering sequence data into the computer and assembling raw sequence data into a contiguous sequence are described first, followed by a description of methods of analyzing and manipulating sequences‐‐e.g., verifying sequences, constructing restriction maps, designing oligonucleotides, identifying protein‐coding regions, and predicting secondary structures. This unit also provides information on the large amount of software available for sequence analysis.The appendix to this unit lists some of the commercial software, shareware, and free software related to DNA sequence manipulation. The goal of this unit is to serve as a starting point for researchers interested in utilizing the tremendous sequencing resources available to the computer‐knowledgeable molecular biology laboratory.

     
 
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Table of Contents

  • Sequence Data Entry
  • Sequence Data Verification
  • Restriction Mapping
  • Prediction of Nucleic Acid Structure
  • Oligonucleotide Design Strategy
  • Identification of Protein‐Coding Regions
  • Homology Searching
  • Genetic Sequence Databases and Other Electronic Resources Available to Molecular Biologists
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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