Setup/Select Genes & Domains Dialog

Use the Gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. & Domain Editor to inspect, define, and select domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog.RH_Domains, and genes, RH_Gene and labels for individual sites.

The Genes & Domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. dialog consists of two tabs: Define/Edit/Select and Site Labels.

Define/Edit/Select tab

This tab contains a hierarchical listing of gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. and domain names with the corresponding information organized into four columns for amino acid sequences and six columns for nucleotide sequences. 

Gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. and domain name listing

Each line in this display contains a small 'expand/contract' box, a checkbox, a gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected./domain icon, and the name of the gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. or domain. The 'expand/contract' box allows you to display or hide the information below a given gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected.. The checkbox shows if the gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. or domain is currently selected for analysis.  All defined genes and domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. appear below the Genes\Domain node in the hierarchy.  All domain names are shown with a yellow background.  The Independent node shows the number of Independent sites In a sequence alignment, all sites that have not been assigned to any gene or domain are classified as independent.RH_Independent_Sites, which are not assigned to any domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. or genes.

If your input data file does not contain any domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., then MEGA automatically creates a domain called Data.  If you wish to create new domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., you should delete the Data domain to make all sites independent.  Remember that only independent sites In a sequence alignment, all sites that have not been assigned to any gene or domain are classified as independent. can be assigned to domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., and sites cannot be assigned to multiple domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog..  Genes are simply collections of domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., and thus gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. boundaries are decided based on the domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. contained in them.  The MEGA gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. and domain organizer is flexible and is designed to enable you to specify genes and domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. as they appear in a genome.  For instance, a sequence may contain one or more genes, each of which may contain one or more domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog..  In between genes, there may be inter-genetic domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog..  In addition, within or between genes or domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., there may be sites that are not members of any domain.

At the bottom of this tab, you will find a toolbar with many drop-down menu buttons, which can be used to Add/Insert new genes or domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog..  The add and insert operations differ in the following way.  If you add a gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. or domain, then the new gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. or domain will be added at the end of the list to which the currently focused gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. or domain belongs.   If you insert a gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. (or domain), it will be inserted by shifting all the following genes or domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. down.  Add and Insert commands are context sensitive.

You can rearrange the relative position of genes and domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. by drag-and-drop operations. 

Inspecting/modifying attributes of genes and domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog.

When you start, all genes and domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. are shown.  Click on the ‘+’ in the expand/contract box to expand the listing for each gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. to its domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog.. Click on the ‘-‘ to collapse to the gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected.. To select and deselect genes or domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. from analysis, click in the corresponding checkbox. When a gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. is selected but some domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. within the gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. are not, the checkbox for the gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. will be grayed. If you deselect a gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected., all domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. within that gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. are automatically deselected.

On the right side of the gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. and domain hierarchy, you will find at least four columns of information for each domain and gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected..  All information shown for genes is computed based on the domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. contained.

The first two columns show the site number in the sequence where the domain begins (From column) and where it ends (To column).  The total number of sites shown next to the To column indicates the total number of sites automatically computed, based on the range of information given in the previous two columns.  A question mark (?) shows that the domain exists but that the range of sites is not yet specified.

To specify or change sites that belong to a given domain, click on the domain name.  The corresponding rows in the From and the To columns contain a button with three dots (ellipses).  To change the start site, click on the ellipses in the From column. This will bring up a small Site Picker dialog box with which you can highlight the desired site and click OK.  In this viewer, you will see that sites have different background colors.  A white background marks independent sites In a sequence alignment, all sites that have not been assigned to any gene or domain are classified as independent., a red background indicates that the site is used by another domain, and a yellow background shows that the current site belongs to the domain being edited.  To cancel any changes, click on Cancel in the Site Picker dialog box.

For nucleotide sequences, two additional columns are found in the Define/Edit/Select tab:  the Coding? column and the Codon A codon is triplet of nucleotides that codes for a specific amino acid. Start column.  A check-mark in the Coding? column shows that a given domain is protein coding.  If it is checked, then the next column allows you to specify whether the first site in the domain is in the first, second, or the third codon A codon is triplet of nucleotides that codes for a specific amino acid. position.

Site Labels Tab

This tab displays sequences and allows you to label individual sites.  To do this, change the default underscore (_) in the topmost line to the labelRH_Labeled_Sites of choice and give it a light green background.  The site number will be displayed below in a window, next to which is shown the name of the domain, along with gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected., name.   Labeled sites Sites in a sequence alignment can be categorized and labeled with user-defined symbols. Each category is represented by a letter or a number. Each site can be assigned to only one category, although any combination of categories can be selected for analysis. Labeled sites work independently of and in addition to genes and domains, thus allowing complex subsets of sites to be defined easily. can be selected or deselected for analysis.

To change or give a label to a site, click on the site and type in the character you wish to mark it with. You can use the left and right arrow buttons on the keyboard to move to and then label adjacent sites. To change a label, simply overtype it. To remove a label, use the spacebar to type a space.

Example 

Imagine an alignment consisting of a genomic sequence, including a gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. and its upstream and downstream regions. You can define each intron Introns are the non-coding segments of DNA in a gene that are interspersed among the exons. and exon A protein-coding gene typically consists of multiple coding regions, known as exons, interspersed with non-coding DNA (introns) as a domain, and then define the overall gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected., assigning the exons and introns to that gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected.. The upstream and downstream regions also can be defined as domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., or possibly multiple domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog., depending on the analysis you wish to perform. These domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. do not have to be assigned to any gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected.. Furthermore, some sites may be left unassigned, as independent sites In a sequence alignment, all sites that have not been assigned to any gene or domain are classified as independent.. These can be scattered throughout the sequence and can be included or excluded from analysis as a group.  If you have a complicated patterns of sites you wish to analyze as groups, and the domain gene A gene is a collection of domains. The domains included in a gene need not be consecutive or of the same type. Genes and domains can be defined in the input data, and can be defined and edited in the Setup Genes and Domains dialog. Genes can be selected or unselected from an analysis. When a gene is unselected, all its domains are automatically unselected. However, a gene can be selected, with some of its domains unselected. approach is unsuitable, you should assign a category to these sites, which can be specified in addition to the groups and domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog..