Sip can read sequence libraries in EMBL, SWISSPROT, GenBank and PIR formats if they have the required index files; and "personal" files in plain text, "Staden", EMBL, Genbank, PIR, FASTA and GCG formats. If supported by the format, personal files can contain multiple entries preceded by entry names. As is explained below a browser is available for selecting entries from such files. Also, unlike our earlier analytical programs, the file format is worked out automatically.

New sequences are entered into SIP using the "Get sequences" option in the File menu. Additional sequences can be entered using the similar "Get horizontal sequence" and "Get vertical sequence" commands. All these options allow DNA or protein sequences to be read in from either sequence libraries or personal files. The available sequence libraries are listed under the first option button and will vary from site to site. This button also allows the selection of personal files. Next to this menu button is the filename entry box which is used for the personal filename. The Browse button next to this will invoke a file browser. See section `Introduction' in filebrowser.. These boxes will be activated if the "personal file" option is chosen from the library menu button. To the right of the file browser button is a "EntryName" / "AccessionNumber" selection menu and the entry box next to this should be completed with either an entryname or accession number accordingly. The final Browse button will invoke the sequence library browser if a sequence library has been selected or an archive browser if searching a personal file.

Hitting the OK button will read the sequences into SIP. If either sequence could not be found, the warning bell will sound and an error will be printed in the Error window, indicating which sequence could not be found. If one sequence failed, try again using either the "Get horizonal sequence" or "Get vertical sequence" options in the File menu.

Extract a sequence from a sequence library

For the horizontal sequence:
1. Select the sequence library from the sequence library menu button.
2. Choose to select EntryNames or AccessionNumber from the menu button.
3. If the entryname or accession number is known, enter this in the entrybox to the right.

If the entryname or accession number is not known and you wish to browse the sequence library, click on the "Browse" button to the right of the entrybox. This will display the sequence library browser. See section `Searching' in seqlib. Select the entry you wish to extract from the sequence library using the left mouse button in the entryname listbox and select "Accept" from either the popup menu or "Selected" menu.See section Interface with parent program. The selected entry name or accession number should now have been entered.

Repeat for the Vertical sequence. To fill in the entryname/accession number entrybox for the vertical sequence from the same sequence library browser, "select" the entrybox by clicking the left mouse button inside it. Move to the sequence library browser and select the required entry and then select "Accept".

Extract a sequence from a personal file

Personal files can contain either a single sequence entry or a several entries concatenated togther. All the entries must be of the same format. The only format current supported is the EMBL library format.

1. Selecting "personal file" from the sequence library option button will highlight the "Filename" fields in the dialogue box.
2. Enter the name of the file in the entrybox to the right of "Filename". Clicking on the associated "Browse" button will invoke a file browser See section `Introduction' in filebrowser.
3. If the file only contains a single sequence, leave the second entrybox blank. The sequence will be read in with the same name as the filename. If the file contains several entries, the entry you wish to extract from the file should be entered in the second entrybox. Alternatively, clicking on the "Browse" button to the far right of the dialogue box will invoke a list box containing the available sequences in the file. Double clicking on an item in the list box will update the associated entrybox.