IMPORT/EDIT PROTEIN SEQUENCE


Contents

Description
Viewing Protein Sequences
Editing Facilities
Deletion
Mutation
Insertion
Undo
Output Files
Changing the external database

Description

This task reads in a protein sequence in Swissprot format, either stored locally or when downloaded from a specified database. This sequence can then be edited for future use.

The "Select Database" menu allows you to choose which database you wish to obtain a protein sequence - either locally, or from an external database. The default external database is the Swissprot database located at the EBI (European Bioinformatics Institute), although this can be changed to any database specified (See "Changing the external database").


Viewing Protein Sequences

If the database selected is an external database, such as the EBI/SwissProt database, specify the accession code in the "Type Protein Code" box and then press the "Import Sequence" button. A message will appear showing an attempt to connect to the external database specified. If the connection is successful, the sequence of this protein will appear in the "Sequence Only" viewing window.

However, if you wish to view the full details of the selected protein, this can be seen when the "View Full Sequence Entry" viewing window is opened.




Editing Facilities

The interface has the ability to manipulate the protein sequence in the "Sequence Only" viewing window in three ways: Deletion, Mutation and Insertion. There is also a Undo function available.


Deletion

Before any of the editing functions can be carried out, a section of the protein sequence must be highlighted. To do this, enter in the "Search For..." box the sequence within the protein that is to be manipulated. If this substring is located within the protein sequence in view, then it will be highlighted in red when the "Search For..." button is pressed.

While any section of the protein sequence is highlighted, editing can be carried out. So, by pressing the "Delete" button, the previously highlighted section of the protein sequence is deleted and a record of this deletion is shown in the viewing window at the bottom of the "Editing" window.




Mutation

The "Mutation" function replaces a highlighted section of the protein sequence with a specified section. In the example below, the first five residues in the protein sequence are replaced by specifying the mutation sequence and pressing the "Mutate into..." button.


Insertion

The "Insertion" function allows the insertion of residues AFTER a highlighted section. In the example below, "YYYYY" is to be inserted after "XXXXX", the first five residues in the sequence. Search for "XXXXX" so it is highlighted, specify the insertion of "YYYYY" and press the "Insert" button.


Undo

The "Undo" function allows the user to undo the last editing function carried out. However, like the other editing functions, this can only be carried out if the search string of the last editing function is highlighted. Otherwise, unwanted changes may occur to the protein sequence.

Output Files

Various files are created while running a job in "Import/Edit Protein Sequence". They are as follows:

*: A copy of the edited sequence, with the filename specified by the user and stored in the specified Project directory.
*. log: Logfile, usually kept in same specified directory and saved file. Shows any problems that might arise during download of the protein sequence.
*. ent: This is a copy of the full SwissProt file of the sequence downloaded. This file does not change if editing is carried out.
*. chg: This file records a list of the changes carried out to the protein sequence.

Changing the external database

The database from which a SwissProt file is obtained is configurable, i.e. the database from which the protein sequence is obtained can be changed. This is done by using the "Configure Interface" window in the "System Administration" toolbar, located in the main CCP4I window and changing the "Command to retrieve sequence from database" line:

Change this URL to specify where Swissprot files may be downloaded from. However, wget MUST NOT be deleted. Example command lines are:

wget http://www.ebi.ac.uk.cgi-bin/swissfetch which is default
wget http://ca.expasy.org/cgi-bin/get-sprot-entry

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