GDE Menu Overview

Menus provide a way of organizing available programs to make them easier to find, and present the choices available. The greatest strength of GDE is that programs can be added to the menus by inserting a few lines of code into the .GDEmenus file, which is read each time the program starts. As new programs are added, or existing menus changed, the changes are immediately available to all users when GDE starts up. Thus, the menus shown below may not include all programs available.

File menu

The file menu is used for importing and exporting sequence data in various formats.
Open - GenBank, gde flat file and gde format files.
Import Foreign Format - most other file types
Open_XYLEM - XYLEM datasets (see splitdb)

Documentation menu

Click on ViewDocumentation to get a pull-down menu listing useful documentation files.

Edit menu

The Edit menu lists sequence editing tasks. Copy out copies the selected sequences to a file called $HOME/.GDEclipboard. Paste in pastes the contents of that file into the current GDE window. Therefore, Copy out/Paste in can be used to move sequences from one GDE window to another.

DNA/RNA menu

The DNA/RNA menu lists programs for common sequence tasks, such as printing, translation, complementation, and restriction site analysis.

RNA structure menu

The RNA structure menu lists programs for RNA structure prediction.

Protein menu

The protein menu lists programs for structure prediction, amino acid characterization and reverse translation.

Similarity menu

The similarity menu lists programs for pairwise comparisons of DNA or protein sequences, using either global alignment or dot-matrix methods.

Database menu

The Database menu lists programs for searching databases using either keyword or sequence information, and for constructing database subset tailored to the user's specifications.

Patterns menu

The Patterns menu lists programs that facilitate the identification of motifs conserved among a group of sequences.

Alignment menu

The Alignment menu lists programs for construction of multiple sequence alignments, as well as programs for display of multiple alignments.

Primers menu

The primers menu lists programs for primer design.

Phylogeny menu

Most programs in the phylogeny menu expect that three of more sequences, aligned by one of the programs in the alignment menu, have been selected. In most programs, output will consist of a report and a treefile. Most menus allow both files to be saved directly to disk (recommended for long running jobs) or to display directly using TREETOOL, DRAWTREE or DRAWGRAM. These three programs can also read in treefiles from disk. Finally, the Phylip help menu item displays individual Phylip documentation files in a textedit window.

Email menu

The email menu lists programs that can be run by email requests to other sites. The selected sequence(s) and parameters are inserted into a mail message which is sent to the remote site. The results return to the user via email. To use GenBank/EMBL Error Report, type in an Accession number. The GenBank entry will be retrieved to one textedit window, and the Error Report form to another window. Using the entry for reference, the error report can be filled in. After saving and quitting the Error report file, the file will automatically by emailed to GenBank or EMBL. An acknowledgement is returned automatically by email within minutes, and the decision of the database annotators will usually be forwarded within a few days.