Most of the items in this menu are used to read and write entries and parts of entries, the exceptions are Clone and Close.
This will open the file manager, or if it is already open will bring it to the foreground. Entries can be dragged from the file manager into the artemis main window and dropped. When dropped the entry is then read in and displayed.
Read an entry (see the section called The "Entry" in Chapter 1), but keep it separate from the others. A new button will be created on the entry button line for the new entry. The new entry will be marked as active (see the section called The Active Entries in Chapter 1) and will be the new default entry (see the section called The Default Entry in Chapter 1).
This function only reads the feature section of the input file - the sequence (if any) is ignored.
Artemis can read these feature file formats:
The output of MSPcrunch. MSPcrunch must be run with the -x or -d flags.
The output of blastall version 2.2.2 or better. blastall must be run with the -m 8 flag which generates one line of information per HSP. Note that currently Artemis displays each Blast HSP is a separate feature rather than displaying each BLAST hit as a feature.
Read the features from an entry (see the section called The "Entry" in Chapter 1) chosen by the user and then insert them into the entry selected by the user.
Save the default entry to the file it came from, unless the entry has been given a new name, in which case the entry is saved to a file with that name. If the entry has no name, Artemis will prompt the user for a new name. [shortcut key: S]
This item will do the same as "Save Default Entry" for the chosen entry.
This sub-menu contains the less frequently used save functions.
Ask for the name of file to save the given entry to. The name of entry (as displayed in the entry button line) will change to the new name.
This does the same as "Save An Entry As -> New File ...", but will write the features and sequence of the entry in EMBL format. Note that currently the header of a GENBANK entry can't be converted to the equivalent EMBL header (it will be discarded instead).
This does the same as "Save An Entry As -> New File ...", but will write the features and sequence of the entry in GENBANK format. Note that currently the header of a EMBL entry can't be converted to the equivalent GENBANK header (it will be discarded instead).
Writes the features in GFF format and sequence of the entry in FASTA format to a file selected by the user. Note that if you use this function on an EMBL or GENBANK entry the header will discarded.
This does the same as "Save An Entry As -> EMBL Format ...", but will write an entry/tab file that contains only valid EMBL qualifiers (see the section called extra_qualifiers in Chapter 4) and valid EMBL keys (see the section called extra_keys in Chapter 4). It will also check that the start and stop codons of each CDS are sensible, that no two features have the same key and location and that all required EMBL qualifiers are present.
This acts like "Save Default Entry", but save all the entries.
Make a new main window with the same contents as the current window. All changes in the old window will be reflected in the new window, and vice versa. The exception to this rule is the selection (see the section called The Selection in Chapter 1), which is not shared between the old and new window.
Close this window.