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String search

Two string searches are available. One, selected from the "Search" menu on the Output window, produces both graphical and textual output, and the other, selected from the "Search" button in the Sequence display, moves the cursor to the position of the next match. Here we document the use of the first search, and the other is described in section Search.

As shown in the dialogue the user selects the range and strand over which the search should be performed, the minimum percentage match, and the string for which to search. The string can include the NC-IUB symbols shown below and the search is not case sensitive.

              NC-IUB SYMBOLS
 
        A,C,G,T
        R        (A,G)        'puRine'
        Y        (T,C)        'pYrimidine'
        W        (A,T)        'Weak'
        S        (C,G)        'Strong'
        M        (A,C)        'aMino'
        K        (G,T)        'Keto'
        H        (A,T,C)      'not G'
        B        (G,C,T)      'not A'
        V        (G,A,C)      'not T'
        D        (G,A,T)      'not C'
        N        (G,A,C,T)    'aNy'

[picture]

The matches are plotted as vertical lines at the match positions with the heights of the lines in proportion to their score. The matches are also written in the Output window as shown below.

[picture]
(Click for full size image)

============================================================
Wed 12 Nov 17:17:20 1997: string search
------------------------------------------------------------
Position 2611 score 8 percent match 80.000000
 Percentage mismatch  20.0
                 1
          string gggggggggg
                 :: ::: :::
    atpase.dat_r GGAGGGAGGG
              2611

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/nip4_10.html