Open a view window for each selected feature showing it's feature table entry. [shortcut key: V]
Open a view window that will show the current selection. The window is updated as the selection changes, so it can be left open.
When one feature is selected the window will show the text (EMBL, GenBank or GFF format) of the feature, the base composition, GC percentage, correlation score (see the section called Correlation Scores), and the bases and translation of the sequence of the feature.
When two or more features are selected the window will show the text (EMBL, GenBank or GFF format) of the features, the base composition, average GC percentage, average correlation score, minimum/maximum GC content and minimum/maximum correlation score of the feature sequence.
When a range of bases is selected the window will show the base composition, GC content percentage and the bases and translation of the sequence of the feature.
On this sub-menu allows the user to view the results of feature searches that are launched from the run menu in Artemis (see the section called The Run Menu).
Pop up a feature list (see the section called The Feature List) of the CDS showing the gene names (from the /gene qualifier) and the product (from the /product qualifier). This list includes pseudo genes.
Each of the items in this sub-menu each allow the user to view a subset of the active features. An example of a subset is all those features with misc_feature as a key. The features are displayed in a new window that contains a menu bar with possible actions to apply to the subset, and feature list (see the section called The Feature List). Most of the possible actions will apply only to the features in the list. For example "Show Overview" in the View menu (see the section called Show Overview) will include statistics only on the features in the list.
Show those CDS features that have a suspicious start codon. ie. the first codon of the feature isn't ATG (in eukaroytic mode) or ATG, GTG and TTG (in prokaryotic mode). This function is effected by the setting of the "Eukaroytic Mode" option in the main options menu (see the section called Genetic Code Tables in Chapter 2 for more).
Show those CDS features that have a suspicious stop codon. ie. the last codon of the feature isn't one of TAA, TAG or TGA.
Show those features that have a key that isn't valid for EMBL/GenBank entries.
Show those features that are duplicated (ie. features that have the same key and location as another feature). These sort of duplicates aren't allowed by the EMBL database.
Show those CDS features that overlap another CDS feature (on either strand).
Show those features that are missing a qualifier that is required by the EMBL database.
Show those features that have a key chosen by the user.
Show the currently selected features in a new feature list. The contents of the list will remain the same even if selection subsequently changes. This is useful for bookmarking a collection of features for later use.
Open a new window the will show a summary of the active entries and some statistics about the sequence (such as the GC content). [shortcut key: O]
The overview window show the following statistics about the sequence:
Number of bases.
GC percentage.
The number of each nucleotide in the sequence.
GC percentage of non-ambiguous bases - ie. the GC content percentage ignoring bases other than A,T,C and G. This should be the same as the "GC percentage" above.
The overview window also shows the following statistics about the features in the active entries (if there are any features). Note that the "genes" are the non-pseudo CDS features.
Number of features in the active entries (see the section called The Active Entries in Chapter 1).
Gene density - the average number of non-pseudo CDS features per 1000 bases.
Average gene length - the average length of non-pseudo CDS features (not including introns).
Number of non-spliced genes.
Number of spliced genes.
Number of pseudo genes (ie. CDS features with a /pseudo qualifier).
Protein coding (CDS) features.
Protein coding (CDS) bases.
Protein coding percentage - ie. the number of coding bases excluding introns.
Coding percentage (including introns).
A summary of the number of features of each key (type) and their colours.
Open a new window the will show a summary of the features and bases of the forward strand.
Open a new window the will show a summary of the features and bases of the reverse strand.
Create a view window for each selected feature, which shows bases of the feature.
Create a view window for each selected feature, which shows bases of the feature in FASTA format.
Create a view window for each selected feature, which shows amino acids of the feature.
Create a view window for each selected feature, which shows amino acids of the feature in FASTA format.
Show some statistics about each selected feature. On the left on the feature information window is the amino acid composition of the feature. On the right is the codon composition of the feature.
Open a window for each selected feature that shows a plot of the Kyte-Doolittle Hydrophobicity [short name: hydrophobicity], the Hopp-Woods Hydrophilicity [short name: hydrophilicity], and an approximation of the GCG Coiled Coils algorithm [short name: coiled_coil]. (For more detail about the coiled coils algorithm see "Predicting Coiled Coils from Protein Sequences", Science Vol. 252 page 1162.) [shortcut key: W]
Some general information about graphs and plots in Artemis can be found in the section called Graphs and Plots. Configuration options for graphs are described in the section called Options For Plots and Graphs in Chapter 5.