[ssml] Finding Matches using N-term & C-term sequences

[Kevin Karplus]

It sounds like you want to use a tool like phi-blast to do pattern searches.
(see http://www.ncbi.nlm.nih.gov/BLAST/producttable.shtml for a
selection guide to the NCBI programs).  There is a pointer from that
table to documentation about the program:

    Pattern-Hit Initiated (PHI) BLAST is designed to search for
    proteins that contain a pattern specified by the user, AND are
    similar to the query sequence in the vicinity of the pattern. This
    dual requirement is intended to reduce the number of database hits
    that contain the pattern, but are likely to have no true homology
    to the query.

    To run PHI-BLAST, enter your query (which contains one or more
    instances of the pattern) into the "Search" box, and enter your
    pattern into the "PHI pattern" box in the "Options"
    section. Patterns must follow the syntax conventions of
    PROSITE. The documentation on Pattern Syntax is at:
    http://www.ncbi.nlm.nih.gov/blast/html/PHIsyntax.html.