first previous next last contents

Sequence manager

Nip allows more than one sequence to be available to the user. The sequence manager allows the user to perform operations on the sequences which have been loaded into Nip. The same operations can also be invoked from the "Sequences" menu. The sequence manager is invoked from the "File" menu. This command invokes a list box showing all the sequences which have been read in together with their active range and length. The currently active sequence is marked with an asterisk (*).

[picture]

Clicking on the sequence name in the sequence manager with the right mouse button invokes a pop-up menu containing operations which may be performed on that sequence. In the figure shown above it can be seen that the names of several of the sequences start with atpase.dat. The sequence read in was called atpase.dat and the other entries have been created using commands in the pop-up menu. For example the sequence called atpase.dat_c is the complement of atpase.dat. These options are described in greater detail below.

Change the active sequence

To change the currently active sequence, either select the "Sequences" menu or select the sequence from the sequence manager and invoke the pop-up menu by pressing the right mouse button. Select "Active" from the menu. This sequence will now be the active sequence.

Set the range

If you are only interested in a region of a particular sequence, it is possible to specify the start and end positions of this region to create a new entry in the Sequence manager. The new sequence will have the same name as the parent, with the addition of a "_s" plus a unique number.

Complement sequence

This function will reverse and complement nucleic acid sequences. Select the "Complement" command from either the "Sequences" menu or the sequence manager pop-up menu. A new sequence will be added to sequence manager list box with the same name as the parent but with "_c" appended to the end.

Interconvert t and u

This function interconverts T and U characters i.e. between DNA and RNA. A new sequence is added to the sequence manager list box with the same name as the parent but the addition to the end of "_r".

Translate sequence

Select the "Translate" command from the either the "Sequences" menu or the sequence manager pop-up menu. It is possible to translate in any particular frame by selecting the appropriate check box. For each translation, a new sequence will be added to the sequence manager list box with the same name as the parent but with the addition to the end of either "_rf1", "_rf2" or "_rf3" to signify reading frames 1, 2 or 3 respectively.

Finally, the "all together" option will produce a single new sequence in the sequence manager, with the extension "_rf123".

Scramble sequence

This function produces a version of a given DNA sequence in which the characters are randomly reordered. i.e. the new sequence has the same length and composition as the original but with the characters in a random order. The new sequence will be added to the sequence manager list box with the same name as the parent except with "_x" plus a unique number appended to the end.

Sequence type

This option allows the selection of the sequence type, ie whether it is linear or circular. The default value is linear.

Rotate sequence

This function allows the user to specify a new origin for a sequence. A new sequence is added to the sequence manager list box with the same name as the parent except with "_o" plus a unique number appended to the end.

Save sequence

To save a sequence to a file, select the "Save" option from either the "File" menu, the "Sequences" menu or the sequence manager pop-up menu. This command invokes a file name entry box. The browse button to the right of the dialogue box invokes a filebrowser (see section File Browser). The sequence is written as plain text.

Delete sequence

To delete a sequence, select the "Delete" option from either the "Sequences" menu or the sequence manager pop-up menu. This command will remove the sequence from the sequence manager and all plots and results that were produced from it.


first previous next last contents
This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/nip4_3.html