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 5) and valid EMBL keys (see the section called extra_keys in Chapter 5). 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.
Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in FASTA format.
Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in PIR format (similar to FASTA, but with a * as the last line of each record).
Prompt for a file name and then write the bases of the selection to that file in the selected format. If the selection consists of features (rather than a base range) then the bases of each feature will be written to the file as a separate record. If the selection is a range of bases, then those bases will be written.
Prompt for a number and a file name, then write that many bases upstream of each selected feature to the file in the selected format. For example if the selected feature has a location of "100..200", then asking for 50 upstream will write the bases in the range 50 to 99. Writing upstream bases of a feature on the complementary strand will work in the expected way.
Prompt for a number and a file name, then write that many bases downstream of each selected feature to the file in the selected format.
Prompt for a file name, then write the complete sequence to that file in the selected format.
Prompt for a file name, then write a codon usage table for the selected features. The file in written in the same format as the data at Kazusa codon usage database site. In the output file each codon is followed by it's occurrence count (per thousand) and it's percentage occurrence. (See the section called Add Usage Plots ... to find out how to plot a usage graph).
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.
Print out the contents of the current window. All or some of the window panels can be select for printing to an image file.
This opens the print image in a preview window. This shows what the image will look like when printed to a file.
This enables the user to define their own shortcut preferences.
Close this window.