Chapter 1 - Contents

• Starting sequence analysis on AGRENET
  • Logging on
  • Starting up the main packages
  • Using LOGIN.COM
  • Other software packages
  • Help information
  • Documentation
  • Graphical output
    • Unipict files
  • Software and database availability on AGRENET
  • Databases on AGRENET
    • Nucleic acid databases
      • Database divisions -
    • Protein databases
    • Brookhaven database
  • Useful VMS commands
  • Queues on AGRENET
    • Batch queues
    • Printer queues

Chapter2 - Contents

• THE GENETICS COMPUTER GROUP PACKAGE
  • 2.1. What is GCG ?
    • 2.1.1. Program examples
    • 2.1.2. Command line modifiers
  • 2.2. Databases with GCG
    • 2.2.1. Database sequence names
    • 2.2.2. Database accession numbers
    • 2.2.3. Searching databases
  • 2.3. Groups of sequences
    • 2.3.1. Files of sequence names
    • 2.3.2. Multiple sequence files
  • 2.4. Program default values
  • 2.5. Graphics with the GCG package
    • 2.5.1. Graphics driver-selection
    • 2.5.2. Fonts
  • 2.6. GCG figure files
  • 2.7. Local data files
    • 2.7.1. Enzyme data files
  • 2.8. Nucleotide symbols in GCG
  • 2.9. Amino acid symbols and the standard translation table
  • 2.10. Nucleotide symbol comparison table for BESTFIT
  • 2.11. PAM250 amino acid symbol comparison table
  • 2.12. BLOSUM62 amino acid symbol comparison table
    • 2.12.1. Analysis of symbol comparison values of PAM250
  • 2.13. Programs in the GCG package (release 7.3)
    • 2.13.1. Supplementary programs

Chapter3 - Contents

• GENERAL SEQUENCE MANIPULATION
  • 3.1. Help information and documentation
    • 3.1.1. GENHELP and EGENHELP - Help on GCG programs
    • 3.1.2. GENMANUAL - Help by program function
    • 3.1.3. EASYGCG - Finding your way
  • 3.2. Formatting a GCG sequence
    • 3.2.1. Formatting raw sequence data
    • 3.2.2. DNA RNA conversion
    • 3.2.3. Sequence complementing
  • 3.3. SEQHELP - Help for other analysis programs
  • 3.4. Copying a database sequence
  • 3.5. Restriction mapping programs
    • 3.5.1. MAP
      • 3.5.1.1. Selecting enzymes -
    • 3.5.2. MAPSORT (and selecting enzymes by region)
      • 3.5.2.1. Digest (and selecting enzymes by name) -
      • 3.5.2.2. Creating a plasmid map. -
    • 3.5.3. The enzyme list
    • 3.5.4. Protein sequence mapping
  • 3.6. Sequence editing
    • 3.6.1. Editing modes -
    • 3.6.2. Adding sequence data from a file -
    • 3.6.3. Moving around in the sequence -
    • 3.6.4. Editing comments -
    • 3.6.5. Writing part of the sequence to a file -
    • 3.6.6. Deleting part of the sequence -
    • 3.6.7. Help -
    • 3.6.8. Exiting -
    • 3.6.9. Changing your keyboard -
  • 3.7. Interconverting sequence formats
    • 3.7.1. Readseq
    • 3.7.2. PIR/NBRF format conversions
    • 3.7.3. STADEN format conversions

Chapter5 - Contents

• PROTEIN ANALYSIS
  • 4.1. Identifying open reading frames
  • 4.2. Identifying potential coding regions
    • 4.2.1. Base composition of bulk DNA
    • 4.2.2. Base composition in the third codon position
    • 4.2.3. Codon usage bias
  • 4.3. Translating RNA into protein
    • 4.3.1. Three and one-letter abbreviations
  • 4.4. Predicting secondary structure in proteins
    • 4.4.1. PEPTIDESTRUCTURE & PLOTSTRUCTURE
    • 4.4.2. MOMENT
    • 4.4.3. PEPPLOT
  • 4.5. Translating protein intoRNA
    • 4.5.1. Best sequence option
    • 4.5.2. Most ambiguous sequence option

Chapter5 - Contents

• COMPARING SEQUENCES
  • 5.1. Identifying sequence homology
    • 5.1.1. Word comparison
    • 5.1.2. Dotplotting
      • 5.1.2.1. Interpreting the plot -
      • 5.1.2.2. The effect of word size -
      • 5.1.2.3. Types of patterns -
    • 5.1.3. Window comparison
    • 5.1.4. Comparison of proteins
    • 5.1.5. Symbol comparison tables
  • 5.2. Sequence alignments
    • 5.2.1. BESTFIT
    • 5.2.2. GAP
    • 5.2.3. Protein sequence alignment
    • 5.2.4. Alignment measurements
      • 5.2.4.1. Quality
      • 5.2.4.2. Ratio
      • 5.2.4.3. Identity
      • 5.2.4.4. Similarity

Chapter6 - Contents

• SEARCHING DATABASES
  • 6.1. Searching by text - STRINGSEARCH
    • 6.1.1. Definition search
    • 6.1.2. Full text search
  • 6.2. Interactive text searches - XQS
    • 6.2.1. Nucleotide databases
    • 6.2.2. Protein databases
  • 6.3. Sequence homology search
    • 6.3.1. FASTA (direct search)
    • 6.3.2. TFASTA (translation search)
    • 6.3.3. Exhaustive homology searching
  • 6.4. Interpreting FASTA output
    • 6.4.1. The FASTA algorithm
      • 6.4.1.1. Disadvantages of the FASTA algorithm -
    • 6.4.2. A FASTA strategy
    • 6.4.3. Diagram of FASTA algorithm
    • 6.4.4. The histogram
    • 6.4.5. Mean scores and cpu time
    • 6.4.6. Example FASTA histogram:
    • 6.4.7. The best scores
    • 6.4.8. The alignments
  • 6.5. Interpreting PROSRCH output
    • 6.5.1. Data check
    • 6.5.2. Symbol comparison table
    • 6.5.3. Additional information
    • 6.5.4. How PROSRCH works
    • 6.5.5. Figure: score vs log (number of entries).
    • 6.5.6. The score distribution and statistics
    • 6.5.7. The alignments
    • 6.5.8. The individual alignment scores
    • 6.5.9. Score ratios and PAM tables
    • 6.5.10. Mapping
    • 6.5.11. Additional alignments
    • 6.5.12. A PROSRCH strategy
  • 6.6. Other Biosearch programs

Chapter7 - Contents

• MULTIPLE SEQUENCE ALIGNMENT
  • 7.1. Cluster alignments
    • 7.1.1. PILEUP
    • 7.1.2. GCLUSTALV
  • 7.2. Manual alignment
  • 7.3. Alignments displays
    • 7.3.1. Threshold, plurality and weightings
  • 7.4. Boxed graphic displays
    • 7.4.1. PRETTYPLOT
    • 7.4.2. PRETTYBOX

chapter8 - Contents

• FRAGMENT ASSEMBLY SYSTEM
  • 8.1. Introduction
    • 8.1.1. Goals
    • 8.1.2. Summary of programs
  • 8.2. Fragment assembly tutorial
    • 8.2.1. NEWGELSTART
    • 8.2.2. GELENTER
    • 8.2.3. GELMERGE
    • 8.2.4. GELVIEW
    • 8.2.5. GELASSEMBLE
    • 8.2.6. GELOVERLAP
    • 8.2.7. GELENTER as an editor
    • 8.2.8. Redefining the project
    • 8.2.9. Detecting vector the unofficial way

chapter9 - Contents

• FINDING SEQUENCE MOTIFS
  • 9.1. Locating partial sequences
  • 9.2. Protein motifs
    • 9.2.1. Retrieving PROSITE documentation

Chapter10 - Contents

• SEQUENCE PROFILING
  • 10.1. The profiling method
  • 10.2. Description of the profile table
    • 10.2.1. A profile as a symbol comparison table
  • 10.3. Finding a new member of the alignment
  • 10.4. Profiling tutorial
    • 10.4.1. PROFILEMAKE
    • 10.4.2. PROFILEGAP
    • 10.4.3. PROFILESEARCH
    • 10.4.4. PROFILESEGMENTS
    • 10.4.5. PROFILESCAN
  • 10.5. Nucleotide profiling

Chapter11 - Contents

• RNA SECONDARY STRUCTURE
  • 11.1. Identifying inverted repeats
  • 11.2. Calculating RNA folding
  • 11.3. Display of folding structures
  • 11.4. Alternative structures

Chapter12 - Contents

• GCG COMMAND FILES
  • 12.1. What are they?
  • 12.2. Editing GCLUSTALV.COM
  • 12.3. STRINGSEARCH
  • 12.4. Other command files

Chapter13 - Contents

• GCG DATA FILES
  • 13.1. Local data files
    • 13.1.1. Enzyme tables
    • 13.1.2. Codon usage (or codonpreference) tables
    • 13.1.3. Symbol comparison tables
    • 13.1.4. Translation tables
    • 13.1.5. Yet more data!!
  • 13.2. PLASMIDMAP files
    • 13.2.1. Displaying blocks and ranges

Chapter14 - Contents

• ORGANISING YOUR OWN DATABASES
  • 14.1. Using files of sequence names
  • 14.2. Create an indexed database

chapter15 - Contents

• PHYLOGENY INFERENCING
  • 15.1. Starting Phylip
  • 15.2. MSF to Phylip
  • 15.3. The DNADIST program
  • 15.4. The NEIGHBOR and FITCH programs

chapter16 - Contents

• BEYOND GCG...
  • 16.1. Submitting a sequence to the databases
    • 16.1.1. Copy the submission form
    • 16.1.2. Enter the details
    • 16.1.3. Mail the sequence
    • 16.1.4. Acknowledgement
    • 16.1.5. Authorin
  • 16.2. Obtaining software from remote sites
    • 16.2.1. The EMBL file server
    • 16.2.2. The Indiana ftpsite
  • 16.3. BIOSCI bulletin board
    • 16.3.1. Topics
    • 16.3.2. Subscription requests
    • 16.3.3. Sending a message to a bulletin board.
    • 16.3.4. Reading the bulletin board
    • 16.3.5. Cancelling subscriptions
    • 16.3.6. Biosci and local bulletins on Agrenet
  • 16.4. The Internet GOPHER
  • 16.5. MOSAIC- world tours by mouse

Appendixa - Contents

• DATABASE SEARCH RESULTS
  • A.1 FASTA search of EMBL37 (Dec 1993) with a word size = 6
    • A.1.1 Histogram
    • A.1.2 The 100 best scores
    • A.1.3 The alignments
  • A.2 FASTA search of EMBL37 (Dec 1993) with a word size = 1
    • A.2.1 Histogram
    • A.2.2 The 100 best scores
  • A.3 TFASTA search of EMBL37 (Dec 1993) with a word size = 1
    • A.3.1 Histogram
    • A.3.2 The 100 best scores
    • A.3.3 A TFASTA alignment

appendix b - Contents

• MISCELLANEOUS
  • B.1. Sequences used in the exercises
    • B.1.1 Main example mRNA sequence.
    • B.1.2 Other RNA sequences
    • B.1.3 Protein sequences
  • B.2. Further reading
  • B.3. Local program amendments
    • B.3.1 Program symbols
    • B.3.2 Batch queue command line option
    • B.3.3 Batch log files
      • B.3.3.1 CLSUBMIT.FOR differences listing:
    • B.3.4 GCLUSTALV
    • B.3.5 STRINGSEARCH and PROFILESEARCH
  • B.4. Obtaining this document from the EMBL file server
  • B.5. WORD for Windows source files

Without a title - Contents

• DOTPLOT DIAGRAMS
  • C.1 A sequence compared to itself
  • C.2 Sequence divergence
  • C.3 Deletions and insertions
  • C.4 Tandem duplication
  • C.5 Internal repeats

Appendixd - Contents

• USING A SEQUENCE DIGITISER
  • D.1. DIGISEQ
  • D.2. Interpretation of sequence gels
    • D.2.1. Band distribution
    • D.2.2. Variable band intensity
      • 1 D.2.2.1The C rules: -
      • 2 D.2.2.2.The A rules: -
      • 3 D.2.2.3.Other rules: -
  • D.3. KERMIT file transfers
  • D.4. EMUTEK file transfers