
<section>
  <title>Introduction</title>
  
  <para>One of the most basic data structures which needs to be
    represented in many bioinformatics applications is the biological
    sequence. The sequence is a relatively simple data structure being
    at heart an ordered sequence of elements, or in otherwords a
    list, which is one of the "standard" data structures in computer
    programming. </para>

  <para>The Java language provides an relatively expensive API for
    representing various data structures, known as the "Collections"
    API. This includes several implementations of Lists. We decided
    however that are several limitations to this representation for
    use in the sequence API. <![%draft;[I need to discuss
    this more in a later section]]> In this document we
    dicuss the design and default implementation of an API which we
    believe can form the basis for representing biological sequences
    within applications using the Java language.</para>

</section>


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