Artemis project view manual

The functions will ask the user for an accession number and then will attempt to read it directly from the EBI using Dbfetch. This menu item will close all windows and then exit the program. Choosing this menu item will discard the current options settings and then re-read the options file.

Note that changing the font size in the file and then selecting this menu item will only change the font size for new windows, not existing windows. Currently some options are unaffected by this menu item. See the section called Options File Format in Chapter 6 for more information about options. This menu item will toggle "direct editing" option.

It is off by default because it can have surprising results unless the user is expecting it. See the section on "Direct Editing" in Chapter 3 for more detail about this.

The default setting is the Standard Code. This setting effects the display of start codons see the section called Start Codons in Chapter 3 and the "Suspicious Start Codons This is an advanced option that can be used to turn off warning message. When this option is on and the "One Line Per Entry" is on see the section called One Line per Entry in Chapter 3 the line that the active entry is on will be highlighted in yellow.

Show the log of informational messages from Artemis. The logging is controlled by log4j. The log4j. This can be used to send the logging information to other places such as a file. Hide the log of informational messages. This window is the main editing and viewing window.

See the section called Open The following images show a breakdown of the main Artemis edit window. The menus for the main window described later in this chapter.

A one line summary of the current selection see the section called The Select Menu and the section called The Selection in Chapter 1 for more. This line contains one button for each entry that has been loaded. These buttons allow the user to set the default entry see the section called The Default Entry in Chapter 1 and to set the active entries see the section called The Active Entries in Chapter 1.

For more detail on operating the buttons see the section called The Entry Button Line. This shows an overview of the sequence and the features from the active entries. This is called the "DNA view" to distinguish it from the overview, but in fact it operates in a very similar way.

A textual summary of the active features. See the section called The Feature List in Chapter 3. 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. 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.

These files need to be indexed as described below. Some examples can be found here. The index file should be in the same directory as the BAM file. This provides an integrated BamView panel in Artemis, displaying sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded in from here either by selecting each file individually or by selecting a file of path names to the BAM files.

BamView will look to match the length of the sequence in Artemis with the reference sequence lengths in the BAM file header. It will display a warning when it opens if it finds a matching reference sequence from these lengths and changes to displaying the reads for that. The reference sequence for the mapped reads can be changed manually in the drop down list in the toolbar at the top of the BamView.

In the case when the reference sequences are concatenated together into one e. It will then adjust the read positions accordingly using the start position of the feature. When open the BamView can be configured via the popup menu which is activated by clicking on the BamView panel. The 'View' menu allows the reads to be displayed in a number of views: stack, strand-stack, paired-stack, inferred size and coverage. In Artemis the BamView display can be used to calculate the number of reads mapped to the regions covered by selected features.

In addition the reads per kilobase per million mapped reads RPKM values for selected features can be calculated on the fly. Note this calculation can take a while to complete. They can be created, sorted and indexed using SAMtools. The VCF files need to be compressed and indexed using bgzip and tabix respectively see the tabix manual and download page.

The compressed file gets read in e. They then get displayed in separate rows in the VCF panel. For single base changes the colour represents the base it is being changed to, i. T black, G blue, A green, C red. There are options available to filter the display by the different types of variants.

Right clicking on the VCF panel will display a pop-up menu in which there is a 'Filter This opens a window with. This can be used to show and hide synonymous, non-synonymous, deletion grey , insertion magenta , and multiple allele orange line with a circle at the top variants. In this window there is a check box to hide the variants that do not overlap CDS features.

There is an option to mark variants that introduce stop codons into the CDS features with a circle in the middle of the line that represents the variant. There are also options to filter the variants by various properties such as their quality score QUAL or their depth across the samples DP.

Placing the mouse over a vertical line shows an overview of the variation as a tooltip. Also right clicking over a line then gives an extra option in the pop-up menu to show the details for that variation in a separate window. There are also alternative colouring schemes.

It is possible to colour the variants by whether they are synonymous or non-synonymous or by their quality score the lower the quality the more faded the variant appears. There is an option to provide an overview of the variant types e. These sequences can be used as input for multiple sequence alignment tools. 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.

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 saves a file in Sequin table format which is used by Sequin. 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. 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 " 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 its occurrence count per thousand and it's percentage occurrence. See the section called Add Usage Plots Make a new main window with the same contents as the current window. All changes in the old window. 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 selected for printing to an image file. These images can be converted to a raster image e. Therefore the SVG format can be useful for creating publication quality figures. The other formats available png , jpeg etc and are raster or bitmap images. This option can be used to print the contents of the current window to a file as PostScript or to a printer. 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. The items in this menu are used to change which entry is the default entry and which entries are active see the section called The "Entry" in Chapter 1. At the bottom of the menu there is a toggle button for each entry which controls whether the entry is active or not.

These toggle buttons work in a similar way the the buttons on the entry button line see the section called The Entry Button Line. Here is a description of the other menu items:.

Set the name of an entry chosen from a sub-menu. The name of the entry is used as the name of the file when the entry is saved. Set the default entry by choosing one of the entries from the sub-menu. See the section called The Default Entry in Chapter 1. Remove an entry from Artemis by choosing one of the entries from the sub-menu.

The original file that this entry came from if any will not be removed. Remove the entries that are currently active. See the section called The Active Entries in Chapter 1.

Choosing this menu item will deactivate all entries. The items in this menu are used to modify the current selection see the section called The Selection in Chapter 1.

Artemis shows a short summary of the current selection at the top of the main window see 2 for details.. Open a new Feature Selector window. The Select button will set the selection to the contain those features that match the given key, qualifier and amino acid motif combination.

The View button will create a new feature list see the section called The Feature List containing only those features that match the given key, qualifier and amino acid motif combination. Reset the selection so that nothing is selected then select all the features in the active entries. Reset the selection so that nothing is selected then select all the bases in the sequence.

Select all features that have no corresponding match in ACT. This is used to highlight regions that are different between sets of sequence. It will only take into account matches that have not been filtered out using the score, identity or length cut-off. Clear the selection so that nothing is selected.

Ask the user for a feature key, reset the selection so that nothing is selected, then select all the features with the key given by the user. Select all the features that have the same key as any of the currently selected features. Extend the current selection of bases to cover complete open reading frames. Selecting a single base or codon and then choosing this menu item has a similar effect to double clicking the middle button on a base or residue see the section called Changing the Selection from a View Window in Chapter 3 for details.

Select those and only those features that overlap the currently selected range of bases or any of the currently selected features. The current selection will be discarded. Select those and only those features that are fully contained by the currently selected range of bases or any of the currently selected features. Ask the user for a range of bases, then select those bases. The range should look something like this:. If the first number is larger than the second the bases will be selected on the forward strand, otherwise they will be selected on the reverse strand unless there is a complement around the range, in which case the sense is reversed.

Ask the user for a range of amino acids in the selected feature and select those bases. The range should look something like this: , or Invert the selection - after choosing this menu item the selection will contain only those features that were not in the selection beforehand.

Open a view window for each selected feature showing it's feature table entry. 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 on Correlation Scores in Chapter 3 and the bases and translation of the sequence of the feature.

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 The Run Menu.

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. 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 in Chapter 3.

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 Overview will include statistics only on the features in the list. Show those CDS features that have a suspicious start codon. 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. Show those features that are duplicated ie. These sort of duplicates aren't allowed by the EMBL database. 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. The overview window show the following statistics about the sequence:. 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. 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. Feature Amino Acids. 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. Some general information about graphs and plots in Artemis can be found in the section called Graphs and Plots in Chapter 3. Configuration options for graphs are described Artemis Option Descriptions in Chapter 6.

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 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.

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 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 an 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 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. 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.

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Feel free to use the FORUM to share useful ideas with the community or, if you prefer, send us an e-mail to:. III Lead Programmer. With Artemis missions, NASA will land the first woman and first person of color on the Moon, using innovative technologies to explore more of the lunar surface than ever before.

We will collaborate with commercial and international partners and establish the first long-term presence on the Moon. Then, we will use what we learn on and around the Moon to take the next giant leap: sending the first astronauts to Mars.

While maintaining American leadership in exploration, we will build a global alliance and explore deep space for the benefit of all. Artemis missions enable a growing lunar economy by fueling new industries, supporting job growth, and furthering the demand for a skilled workforce. We will explore more of the Moon than ever before with our commercial and international partners. Along the way, we will engage and inspire new audiences — we are the Artemis Generation.