Section 1-2: How to Use this Guide

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Conventions

This guide uses the convention to have a generic example command printed like:

% logout

Whereas specific examples are printed like:

 

  
 % ls -lsat 
  

  

The JAMF code produces a set of HTML files which are indexed and listed accordingly. The JAMINX.HTML file is the startup page.

The auxiliary file BIOCOMPANION.TEX (part of the distribution) has to be used in the LATEX processor (adopt margins if you do not use European DIN A4 format). Before rerunning LATEX the second time you need to run the 'makeindex' program which should generate the file BIOCOMPANION.IND. This file is not part of the original distribution, thus, possibly generates an error message in the first run.

Load the RTF file in your preferred word processor. (Be sure that this one can digest over 100 pages, and be prepared to wait.) You might consider producing several small files instead of one big file, but this will hinder indexing afterwards. In any case, add line numbers at the bottom of the page (JAMF RTF files have the header with the chapter name in it). Next, jump to the end of the file and add the Chapter Index. You might need to select an 'options' box in order to accommodate the 'Table Entry Fields' as the JAMF program does not produce 'Header Styles' (i.e., it uses .c. paragraphing). Last, generate a keyword index with the index creation tool. Save the file as Word Processor file and print this file only after reopening it.

This document does provide 13 exercises which shall help the reader to validate the understanding of the read explanations. The last four are 'advanced' exercises. In order to practice, the reader must have access to a system which runs a licensed GCG installation .

Exercise Topic

• 1. WPI exercise: Run a 'fasta' search

• 2. Editor exercise: Type in a DNA sequence

• 3. Editor exercise: Create a DNA sequence fragment

• 4. Hunting exercise: Find the DNA alphabet in the documentation

• 5. DNA composition: Determine the G/C content of a DNA sequence

• 6. DNA reading frame analysis: Prediction of an ORF

• 7. Summary of single-sequence protein analysis tools

• 8. Schematic pairwise DNA analysis: Compare two sequences

• 9. Internal repeat analysis: Analyse a single sequence

• 10. Pairwise sequence analysis: Comparison matrices

• 11. Patterns: Use of the motif searching program

• 12. Sequence searching: Use of the 'blast' and 'fasta' searching programs

• 13. Understand the benefit, scope and limitations of a rigorous searching method.