The items in this menu allow the user to navigate around the sequence and features.
Open a new navigation window. [shortcut key: G]
This window allows the user to perform five different tasks:
Scroll all the views so that a particular base is in the centre of the display . To use this function, type a base position into the box to the right of the "Goto Base:" label then press the goto button at the bottom of the window. The requested base will be selected and then the overview display and the DNA display will scroll so that the base is as near as possible to the middle of the main window.
Find the next feature that has the given gene name . To use this function, type a gene name into the box to the right of the "Goto Feature With This Gene Name:" label and then press the goto button. Artemis will select the first feature with the given text in any of it's qualifiers and will then scroll the display so that feature is in view.
Find the next feature that has a qualifier containing a particular string . To use this function, type a string into the box to the right of the "Goto Feature With This Qualifier Value:" label and then press the goto button. Artemis will select the first feature with the given string in any of it's qualifier values (see the section called EMBL/Genbank Feature Qualifiers in Chapter 1) and will then scroll the display so that feature is in view.
Find the next feature that has a particular key . To use this function, type a key into the box to the right of the "Goto Feature With This Key:" label and then press the goto button. Artemis will select the first feature with the given key and will then scroll the display so that feature is in view.
Find the next occurrence of a particular base pattern in the sequence . To use this function, type a base pattern into the box to the right of the "Find Base Pattern:" label and then press the goto button. Artemis will select the first contiguous group of bases on either strand that match the given base pattern and will then scroll the display so that those bases are in view. Any IUB base code can be used in the pattern, so for example searching for aanntt will match any six bases that start with "aa" and ends with "tt". See Table 3-1 for a list of the available base codes.
Find the next occurrence of a particular residue pattern in the sequence . To use this function, type a amino acid pattern into the box to the right of the "Goto Amino Acid String:" label and then press the goto button. Artemis will select the first contiguous group of bases on either strand that translate to the given amino acids and will then scroll the display so that those bases are in view. The letter 'X' can be used as an ambiguity code, hence 'AAXXXDD' will match 'AALRTDD' or 'AATTTDD' etc.
Note that for all the functions above except the first ("Goto Base"), if the "Start search at beginning" option is set or if there is nothing selected the search will start at the beginning of the sequence. Otherwise the search will start at the selected base or feature. This means that the user can step through the matching bases or features by pressing the goto button repeatedly.
If the "Ignore Case" toggle is on (which is the default) Artemis will ignore the difference between upper and lower case letters when searching for a gene name, a qualifier value or a feature key.
The "Allow Substring Matches" toggle affects 2 and 3. If on Artemis will search for qualifier values that contain the given characters. For example searching for the genename CDC will find CDC1, CDC2, ABCDC etc. If the toggle is off Artemis will only find exact matches, so searching for the gene CDC will only find features that have /gene="CDC" not /gene="CDC11".
Scroll all the views so that the first base of the selection is as close to the centre as possible. If the a range of bases is selected the views will move to the first base of the range. If one or more features are selected, then the first base of the first selected feature will be centred. Otherwise, if one or more segments (see the section called Feature Segments in Chapter 1) is selected then the first base of the first selected segment will be centred. [shortcut key: control-left]
This does the same as "Goto Start of Selection", but uses the last base of the selected range or the last base of the last selected feature or segment. [shortcut key: control-right]
Scroll the views to the start of the first selected feature.
Scroll the views to the end of the first selected feature.
Scroll the views so that the start of the sequence is visible. [shortcut key: control-up]
Scroll the views so that the end of the sequence is visible. [shortcut key: control-down]
Ask the user for a base position within the first selected feature, then scroll the views so that that base position is centred.
Ask the user for an amino acid position within the first selected feature, then scroll the views so that that position is centred.