The items in this menu allow the user to navigate around the sequence and features.
Open a new navigation window. 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 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 Text:" label and then press the goto button. Artemis will select the first feature with the given string in any of it's qualifier values 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.
Note that for all the functions above except the first ("Goto Bases"), 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.
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.
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.
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.
Scroll the views so that the end of the sequence is visible.
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.