Nip can read sequence libraries that have been indexed either by srs5.1 or EMBL. To change which indices to use, it is necessary to edit the .seqlibrc file, see section the .seqlibrc File. Any format can be read if the relevant srs indices have been created. If EMBL indices are used, then EMBL, SWISSPROT, GenBank and PIR formats can be read. Personal files can be 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. The file format is worked out automatically.
New sequences are entered into Nip using the "Load sequences" option in the File menu. This invokes a cascading menu containing 3 modes of searching, the simple search, sequence library search and a personal archive search (see below).
Each new sequence entered will have its own sequence viewer window. If a sequence is entered which has the same name as one already loaded, its name is changed by the addition of '#number' where 'number' is a unique identifer. For example, if the sequence "hsproperd" has already been loaded and this sequence is loaded again, the name of this second sequence is changed to "hsproperd#0".
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. The second option 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. If a personal file is selected, the filename should be entered in the entrybox. The Browse buttons at the far right of the dialogue box either invoke a library browser, see section Sequence library interface or a file browser,see section File Browser depending on whether a sequence library or personal file has been selected.
This searching mode invokes a library browser,see section Sequence library interface. To load a sequence(s) from the library into Nip, first highlight the entryname(s) required in the entryname listbox using the left mouse button. Once the entries have been highlighted, either press the right mouse button to invoke a popup menu and select "Load" or click on the Load button in the top right hand corner of the dialogue box or pull down the Selected menu and choose "Load". The selected entries should now have been loaded into Nip.
This method invokes an archive browser. Enter the filename of the personal file in the entrybox. The Browse button to the right will invoke a file browser, see section File Browser. If the file contains multiple entries, these will be displayed in the list box. It is necessary to press "Enter" after entering the filename in order for the entries to be displayed. Select the required entryname(s) and press OK. The selected entries should now have been loaded into Nip.