Construct database

The database should contain representatives of the phylogenetic group that the oligonucleotide is supposed to target, along with records outside that target group.  The database can be constructed from one or more sequence files, in GenBank or Fasta format.  Sequences can be aligned or unaligned.  Each sequence should have a unique accession number - if a duplicate is detected the program will reject the existing files.  The program can also use the RDP release 8.1 database, which comes supplied with the program.

Click ' Construct Database' button on main panel.

The following dialog box will appear:



Use this dialog box to collect together all sequence records to be used in the analysis (i.e., sequence records representing the oligonucleotide's target group and a selection of non-target records representing taxa that are supposed to be excluded).  This is achieved as follows:

1) Click ' Load SequenceFile(s)' button on resulting dialog box.

An Open File Dialog box is generated:



Use this dialog to select an RDP release 8.1 database (files with suffix .phylo), or any number of GenBank (.gb) or Fasta (.fas) formatted files.  RDP files can be found in the database directory that is included with the program.

2) Selected files are displayed in the 'Construct Database Dialog'.  Double clicking on a sequence file icon, , displays its contents.



All sequence records (identified by ) displayed in this dialog will be used by the program.  If there are records you wish to exclude, left mouse click (Windows, Linux) or mouse-click + Ctrl (Apple OsX) the record (or group of records) to exclude (excluded records are identifed so: ).  Click here for an icon key.



3) When all required files have been loaded, click 'Accept' button to return to the main window.  'Cancel' button returns to the main window without saving selections.