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Sequence manager

SIP allows more than two sequences to be available to the user. The sequence manager allows the user to perform operations on the sequences which have been loaded into SIP. 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 into SIP together with their ranges, lengths and whether they are DNA (D) or Protein (P). The currently active horizontal and vertical sequences are marked with a "H" and "V" respectively. In the picture below, these are "hsproperd" and "mmproper".

[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. The operations available depends on whether the sequence is DNA or protein.

These options are described in greater detail below.

Change the active sequence

To change the currently active horizontal or vertical 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 "Horizontal" or "Vertical" from the menu. This sequence will now be the active "Horizontal" or "Vertical" 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. The third entry in the picture above shows the range has been set from 100 to 1000, giving a total length of 901 bases for the sequence "hsproperd".

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 the sequence manager list box with the same name as the parent but with "_c" appended to the end. The forth entry in the picture above is the complemented sequence of "hsproperd".

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". The fifth entry is the picture above is the transcribed sequence of "hsproperd".

Translate sequence

This operation is only available for DNA sequences. Select the "Translate" command from 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", exemplified by the ninth entry in the picture above. Although at this point the sequence is still DNA, when it is used in a comparison function the program will translate it automatically into the three reading frames. The important point is that the results from the three reading frames will be superimposed in the plot, hence enabling frameshift errors to be spotted.

For example to compare a DNA sequence in all it's reading frames with a protein:

  1. Convert the DNA sequence using the "all together" command
  2. Select this sequence as horizontal
  3. Select the protein sequence as vertical
  4. Invoke the relevant comparison function

Scramble sequence

This function produces a version of a given DNA or protein 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. The tenth entry in the picture above is the scrambled version of "hsproperd". For long sequences, scrambling and then comparing should produce similar numbers of matches as are predicted by the probability calculations ( see section Probabilities and expected numbers of matches).

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. The eleventh entry in the picture above is of a rotated version of "mmproper". This operation is not allowed for sub-sequences ie those created using "Set range".

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.


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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/sip_5.html