The 'Modules'-menu gives access to additional modules, which are not directly implemented into T-ACE. There are already three modules integrated into T-ACE. These serve as examples for writing new modules. How to write such a module is explained under 'Writing custom modules' at the end of this manual.
The blast result window shows two result sequences. 'Result 1' contains the query match sequence;
'Result 2' the subject match sequence. Additionally, sequence parts from 'Sequence 1' and 'Sequence
2', which do not appear in the blast hit, are attached to the start or end of the result sequences.
By clicking the 'Result 1'-button or 'Result2'-button the according result sequence will be opened in a
'New sequence'-window and can be added to the T-ACE database.
To use this module NCBI-blast+ has to be installed.
The update will create contig lists for each cohort and the reference list, consisting of all contigs of all cohorts. The results of the update will be visualized in the 'Cohort statistics'-tab.
An update is always necessary, when a cohort was added, removed or changed.
After the update is completed the cohorts can be compared against the reference contig list concerning the distribution of GO terms, KEGG terms or protein domains. To do this, select the 'GO'-, 'KEGG'-, or 'Domain'-tab and press the 'Compare'-button in the upper left corner of the tab. The comparing can take several minutes to complete.
The result table of the comparison consists of several columns. The first column shows the GO, KEGG or domain ID, the second column the according name. The third column shows the number of contigs
in the reference, which are associated with the ID in the first column. Then follow always three columns for each cohort. The first cohort column shows the number of contigs in the cohort, which are associated with the ID in the first column. The second cohort column shows the number of contigs that could be expected for the cohort and the third cohort column shows the two-tailed p-value.