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The Tools menu

This menu contains some tools for working with a whole database or just on groups of contigs. The tools 'Primer3' and 'Search repeats' also appear in some right-click menus.

Expression analysis
InterProScan
Phobos
Primer3
Search

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Expression analysis

This function creates a contig list, including the selected kind of annotation description, with the up- or down-regulation level and/or the numbers of reads in groups A and B, included in a contig. The read classification (A or B) depends on the run setting in the 'Database info'-tab.
The contig list can be exported as a tab-delimited text file with the 'Export'-button.

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InterProScan

To use this option InterProScan has to be installed on the same computer as the PostgreSQL server. Additionally Postgres needs execution rights for the iprscan/bin folder and writing rights for the iprscan/tmp folder.
InterProScan is available at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html

The 'InterProScan'-option will try to annotate every checked table entry of the 'Database browser' or a project tab, depending on which tab is raised. The found domains will be written to the database.

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Phobos

Phobos is a tandem repeat search tool. To use the 'Phobos'-function of T-ACE the phobos_cl executable has to be in the system path. Phobos is available at http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm
The 'Phobos'-window allows the setting of most Phobos parameters. The parameters can be saved as standard by clicking the 'Save'-button.
After clicking the 'OK'-button Phobos will search for repeats according to the parameter setting. The found repeats will be written directly into the database.
If the 'Search for repeats'-window was opened through the 'Search repeats'-option of the 'Tools'-menu, than it will search repeats in each checked contig sequence of the 'Database browser' or a project tab, depending on which tab is raised.
The found repeats will be listed in the 'Repeats'-tab.

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Primer3

Primer3 is a tool for designing PCR primers. To use the 'Primer3'-function or, in the right-click menu, 'Create primer'-function of T-ACE the primer3_core executable has to be in the system path. Primer3 is available at http://sourceforge.net/projects/primer3/files/
The 'Create primers'-window allows the setting of most Primer3 parameters. The parameters can be saved as standard by clicking the 'Save'-button.
After clicking the 'OK'-button primers will be generated according to the parameter setting. The created primers will be written directly into the database.
If the 'Create primers'-window was opened through the 'Primer3'-option of the 'Tools'-menu, than it will create primers for each checked contig sequence of the 'Database browser' or a project tab, depending on which tab is raised.
The generated primers will be listed in the 'Primer'-tab.

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Search

With the 'Search'-window it is easy to search in databases for certain key words. The results will be listed in a project tab.
On the left side of the window the, for the search, available databases are listed.
Then comes the feature list, were the user can choose for which types of annotation the search shall be performed.
The three 'Search'-fields allow three different searches in the same search run, the results of all three searches will be listed in the same project tab. All words that are typed into the same 'Search'-field have to appear in the annotation of one of the selected 'Search types', otherwise there will be no hit.

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