T-ACE mainly consists of two parts. The upper part of the window shows information about the database and its contents, the lower part shows detailed information for a single database entry.
Both parts contain several tabs, which will be described in detail in the following sections. Many of the tabs are optional and can be closed through the 'X'-button in the right corner of the tab.
Most of the tables in the tabs possess a menu which can be opened through a click on the right mouse button. Those menus allow changes to the table configuration or the execution of tab specific features. Below you see two examples for such menus. Some options refer to the whole table, such as 'Hide/Show column', 'Hide/Show hits from...' or 'Save table', the other options are normally row specific.
The 'Copy'-option is the most common one and refers always to the selected table cell. It copies the cell content to the clipboard.
Other options, like 'Add to blast' and 'Edit sequence', will be explained in the appropriate chapter.
Before you start working with T-ACE it is necessary to set some variables. To do this open the 'Config'-menu of T-ACE.
The most important setting is the 'Database connection'. Here the user sets the IP-address and port to his postgresql database and the name of the parent database, which were created with the 'T-ACE_DB_manager.tcl'. The user name is not necessary, but the entry will appear as login name when starting T-ACE.
The 'Server authentification' is needed, when T-ACE is used with a php script. The 'Folder' entry, together with the host IP, shows location of the T-ACE.php. In this case the URL to the php script would look like this:
http://127.0.0.1/tace/T-ACE.php
Here you set your standard parameters for the 'Blast'-tab. You can choose to blast with a blast server, by setting an URL, or locally. If you choose the 'Local blast'-option you can only blast against blast-databases which are in the /blast_dbs folder of the T-ACE directory. For the local blast NCBI-blast+ has to be installed.
To set the 'BrowserPath' select the executable of your favored browser. This is important, because some of the tables in T-ACE contain columns with link buttons.
You can find a list of all links in the T-ACE directory under: /conf/links_tace.conf
There you can change existing links or add new ones.
The 'HomeFolder' is standard folder for opening and saving files.
Sets the path to file with information about protein translation codon usage.
Some such files can be found in the T-ACE directory under: /gcodes/
T-ACE contains two types of sequences, nucleotide and protein sequences.
The nucleotide sequences consist of three different subtypes: contigs, reads and singletons
A contig (from contiguous) is a set of overlapping DNA segments (reads), which can be assembled to represent the original DNA sequence of the source.
Here, the word contig is also used to refer to one segment of the original DNA sequence, not necessarily the complete one.
In T-ACE all sequences, which were used in the contig assembly, are called reads. Normally they would be ESTs.
A read, that does not cluster with other reads is called a singleton.