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Sequence display

Each sequence shown in the "Sequence manager" list can have its own "Sequence display" window. The Sequence display provides a way of viewing and scrolling along the characters of the sequence. It can also show translations to protein and the positions of restriction enzyme cutting sites. Movement along the sequence is controlled by standard mouse and cursor commands and by the use of a string search routine. The cursor can also be controlled by dragging the cursor in the programs' graphical displays.

When restriction enzyme cutting sites are shown in the Sequence display window the number of rows of text to be displayed at any position along the sequence varies with the density of the sites. This presents a tricky problem about how to position the lines of text relative to the top and bottom of the window. Should the height of the window grow and shrink vertically as the user scrolls? Should the window maintain a fixed height, in which case should the top or the bottom be clipped if the number of lines of text exceeds the window height? We have programmed it so that the nucleotide sequence remains at a fixed height to provide a constant reference and the user can select this height by use of a vertical scroll bar and by growing or shrinking the window. The scroll bar will allow vertical movement when the number of lines of text exceeds the current window size.

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Search

The Sequence display contains a string search function which moves the cursor to the position of the next match. As shown in the dialogue the user selects the direction and strand over which the search should be performed, the minimum percentage match, and the string for which to search. The string can use any of the NC-IUB symbols shown in the figure below. Once activated the Search dialogue will remain visible until the user clicks on the "Cancel" button. The cursor will move to the next matching position each time the user clicks on the "Search" button, or will "beep" if there is no such match.

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              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'

Save

Saving the contents of the sequence display to a file

The Sequence display contents can be dumped to a file by selecting the "Save" option from the menu. Whatever options are currently activated (i.e. which of restriction enzyme sites, translation, ruler and strands) will be written to disk. The user can define the region of the sequence for which to dump the results and the name of the file to use.

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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_6.html