1. Contents
2. 1. Preface
   1. Rodger Staden, January 1994.
3. 1.1 Preface to third edition (November, 1993)
4. 1.2 Preface to second edition (November, 1992)
5. 1. 3 Preface to first edition (March 1992)
6. 2. Introduction
   1. Table of contents
   2. 1.Introduction
   3. 2.Materials
      1. 2.1Versions.
         1. 2.1.1UNIX version.
         2. 2.1.2Other UNIX versions.
      2. 2.2Terminals.
      3. 2.3Digitizers.
      4. 2.4Sequencing machines and film readers.
   4. 3.User Interfaces
      1. 3.1The xterm interface
         1. 3.1.1.Menus and option selection
         2. 3.1.2Execution and dialogue
         3. 3.1.3Help
         4. 3.1.4.Quitting
         5. 3.1.5.Making selections
         6. 3.1.5.1.Choosing between opposites.
         7. 3.1.5.2. Choosing one from many.
         8. 3.1.5.3.Choosing at least one from many.
         9. 3.1.6.Input of numerical values
         10. 3.1.7.Input of character strings
      2. 3.2.The X interface
      3. 3.3.Use of the bell
      4. 3.4.Printing and saving results in files
      5. 3.5.Use of feature tables
      6. 3.6.Use of graphics
         1. 3.6.1.The drawing board and plot positions
         2. 3.6.2.The plot interval
         3. 3.6.3.The window length
         4. 3.6.4.Use of the cross hair
         5. 3.6.5Drawing scales on plots
         6. 3.6.6Saving graphics
      7. 3.6.7 Postscript files
      8. 3.7.The active region
      9. 3.8.Files of file names
   5. 4.Character Sets
      1. 4.1Character sets for finished sequences
      2. 4.2Symbols used in gel readings
   6. 5.Sequence Formats
      1. 5.1Personal sequence files
      2. 5.2Sequence libraries
      3. 5.2.1 Introduction to the EMBL CDROM indexing method
      4. 5.2.2 Organisation of the sequence library files.
      5. 5.2.3 Installing the sequence libraries.
         1. 5.2.3.1 Installing from the EMBL CDROM
         2. 5.2.3.2 Installing all libraries other than those onthe EMBL CDROM
   7. 6.Conventions Used In The Manual
   8. 7.NOTES
      1. 7.1
   9. 8.References
7. 3. Sequence Input, Editing and Sequence Library Use
   1. Table of contents
   2. 1.Introduction
      1. 1.1Introduction to sequence input and editing
      2. 1.2Introduction to keyboard input
      3. 1.3Introduction to input from digitizer
      4. 1.4Introduction to editing single sequences
      5. 1.5Introduction to using the sequence libraries
   3. 2.Methods
      1. 2.1Sequence input from keyboard
      2. 2.2Sequence input from digitizer
      3. 2.3Sequence input from the Pharmacia A.L.F.
      4. 2.4Sequence input from the ABI 373A.
      5. 2.5Editing a nucleic acid sequence using restriction sites and a translation and base numbering as landmarks.
      6. 2.6Searching the freetext (or author, or taxon) index of a sequence library
      7. 2.7Using accession numbers to retrieve data from a sequence library
      8. 2.8Displaying the annotations for an entry in a sequence library
      9. 2.9Reading a sequence from a sequence library
      10. 2.10Worked example of sequence library access
   4. 3.NOTES
   5. 4.References
8. 4. Managing Sequencing Projects
   1. Table of contents
   2. 1.Introduction
   3. 2.Methods
      1. 2.1Starting a project database
      2. 2.2Screening against restriction enzyme recognition sequences
      3. 2.3Screening against vector sequences and repeat families
         1. 2.3.1Clipping off vector sequences
         2. 2.3.2Screening for "vectors"
      4. 2.3.3 Screening for repeat families
      5. 2.4Entering readings into the project database (Assembly)
      6. 2.5Searching for internal joins
      7. 2.6Editing in XBAP
         1. 2.6.1Scrolling through the contig
         2. 2.6.2Editing operations
         3. 2.6.3Use of buttons
         4. 2.6.4Displaying traces for readings from fluorescent sequencing machines
         5. 2.6.5Extending reads with the hidden data
         6. 2.6.6Using the pop-up menu
         7. 2.6.7Annotating readings
         8. 2.6.8Creating a new annotation
         9. 2.6.9Editing an existing annotation
         10. 2.6.10Deleting an annotation
         11. 2.6.11Searching
         12. 2.6.11.1Search by position
         13. 2.6.11.2Search by reading name
         14. 2.6.11.3Search by tag type
         15. 2.6.11.4Search by annotation
         16. 2.6.11.5Search by sequence
         17. 2.6.11.6Search by problem
         18. 2.6.11.7Search by quality
      8. 2.7Joining contigs interactively using XBAP
      9. 2.8Selecting primers and templates
      10. 2.8.1Selecting primers and templates interactively
      11. 2.9Examining the "quality" of a contig
      12. 2.10Using graphical displays to examine contigs
      13. 2.11Check assembly
      14. 2.12Examining the positions of reads from the same template
      15. 2.13Disassembling and breaking contigs
      16. 2.13.1Disassembling contigs
      17. 2.11.2Breaking a contig
      18. 2.14Finding and labelling repeats
      19. 2.15.Filling single stranded regions with hidden data
      20. 2.16Shuffling pads
      21. 2.16Checking for editing mistakes
      22. 2.18Displaying a contig
      23. 2.19Highlighting differences between readings and the consensus
      24. 2.20Screen editing contigs in SAP
      25. 2.21Automatic editing of contigs in SAP
      26. 2.22Using the original editor in SAP
   4. 3. NOTES
      1. 3.1 Finding the cloning site.
      2. 3.2 Finding the primer site
         1. 3.2.1 The forward primer.
         2. 3.2.2 The reverse primer
      3. 3.3 How to do the calculations in a single step
         1. 3.3.1 The forward primer
         2. 3.3.2 The reverse primer
   5. 4.References
9. 5. Analysing Sequences to Find Genes
   1. Table of contents
   2. 1.Introduction
   3. 2.Methods
      1. 2.1The uneven positional base frequencies method.
      2. 2.2The positional base preferences method
         1. 2.2.1Using the global standard
         2. 2.2.2Using a nonglobal standard
      3. 2.3The codon usage method
      4. 2.4Searching for open reading frames
      5. 2.5Searching for tRNA genes
   4. 3.Notes
   5. 4.References
10. 6. Searching for Motifs in Nucleic Acid Sequences
    1. Table of contents
    2. 1.Introduction
    3. 2.Methods
       1. 2.1Searching for percentage matches to consensus sequences
       2. 2.2Searching for consensus sequences using a score matrix
       3. 2.3Using weight matrices for searching nucleotide sequences
          1. 2.3.1Creating a weight matrix file from a set of aligned sequences
          2. 2.3.2Searching using a weight matrix
       4. 2.4Using "hardwired" motif searches.
          1. 2.4.1Searching for splice junctions
    4. 3.Notes
    5. 4.References
11. 7. Using Patterns to Analyse Nucleic Acid Sequences
    1. Table of contents
    2. 1.Introduction
    3. 2. Methods
       1. 2.1Creating a pattern file containing an exact match motif and weight matrix motif.
       2. 2.2Searching a sequence using a pattern file
       3. 2.3Comparing a sequence against a library of patterns
       4. 2.4Searching sequence libraries for patterns
    4. 3.Notes
    5. 4.References
12. 8. Searching for Restriction Sites
    1. Table of contents
    2. 1.Introduction
    3. 2.Methods
       1. 2.1Search for restriction enzyme sites and list them enzyme by enzyme
       2. 2.2Search for restriction enzyme sites and list them by position
       3. 2.3Search for restriction enzyme sites and list their names above the sequence
       4. 2.4Search for restriction enzyme sites and plot their positions
       5. 2.5Finding restriction enzymes that cut infrequently
       6. 2.6Producing a back translation from a protein sequence
    4. 3.Notes
13. 9. Statistical and Structural Analysis of Nucleotide Sequences
    1. Table of contents
    2. 1.Introduction
    3. 2.Methods
       1. 2.1Calculating the base composition
       2. 2.2Calculating the dinucleotide composition
       3. 2.3Calculating the codon composition
       4. 2.4 Creating a codon usage file
       5. 2.5Plotting the base composition
       6. 2.6Searching for anomalous compositions
       7. 2.7Search for anomalous word usage
       8. 2.8Calculate codon constraint
       9. 2.9Searching for stem-loop structures
       10. 2.10Searching for long range inverted repeats
       11. 2.11Searching for long range repeats
       12. 2.12Searching for repeated words
       13. 2.13Searching for possible Z DNA
    4. 3.Notes
    5. 4.References
14. 10. Translating and Listing Nucleic Acid Sequences
    1. Table of contents
    2. 1.Introduction
    3. 2.Methods
       1. 2.1Listing the sequence with all six reading frames translated
       2. 2.2Listing the sequence with its open reading frames translated
       3. 2.3Listing the sequence with defined segments translated
       4. 2.4Listing the sequence with translated segments defined from a feature table
       5. 2.5Producing a file of protein sequences for all open reading frames.
       6. 2.6Producing a file of protein sequences for segments defined from a feature table
    4. 3.Notes
15. 11. Statistical and Structural Analysis of Protein Sequences
    1. Table of contents
       1. 1.Introduction
       2. 2.Methods
          1. 2.1Plotting hydrophobicity
          2. 2.2Plotting charge
          3. 2.3Plotting hydrophobic moment and hydrophobicity
          4. 2.4Drawing helical wheels
          5. 2.5Producing a Robson secondary structure prediction
          6. 2.6Calculating the composition and molecular weight of a sequence.
       3. 3.Notes
       4. 4.References
16. 12. Searching for Motifs in Protein Sequences
    1. Table of contents
    2. 1.Introduction
    3. 2.Methods
       1. 2.1Searching for exact matches.
       2. 2.2Searching for percentage matches to sequences
       3. 2.3Searching for sequences using a score matrix
       4. 2.4Using weight matrices for searching protein sequences
          1. 2.4.1Creating a weight matrix file from a set of aligned sequences
          2. 2.4.2Searching using a weight matrix
    4. 3.Notes
    5. 4.References
17. 13. Using Patterns to Analyse Protein Sequences
    1. Table of contents
    2. 1.Introduction
       1. 1.1Introduction to the PROSITE motif library
       2. 1.1.1 Browsing through PROSITE.
    3. 2.Methods
       1. 2.1Creating a pattern file containing a weight matrix motif and a membership of a set motif.
       2. 2.2Searching a sequence using a pattern file
       3. 2.3Comparing a sequence against a library of patterns including PROSITE
       4. 2.4Searching libraries for patterns
       5. 2.5Preparing the PROSITE motif library for use by the programs
    4. 3.Notes
    5. 4.References
18. 14. Comparing Sequences
    1. Table of contents
    2. 1.Introduction
    3. 2.Methods
       1. 2.1Producing a dot matrix plot (or list) of exact matches
       2. 2.2Producing a dot matrix plot using the proportional algorithm
       3. 2.3Producing a dot matrix plot using the quick scan algorithm
       4. 2.4Producing a list of all matching segments using the proportional algorithm
       5. 2.5Calculating the expected scores for the proportional algorithm
       6. 2.6Calculating the observed scores for the proportional algorithm
       7. 2.7Producing an optimal alignment
       8. 2.8Comparing a sequence against a library of sequences
    4. 3.Notes
    5. 4.References