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The Modules menu

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.

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Blast align

'Blast align' allows to blast two sequences against each other. It is possible to blast nucleotide or protein sequences.

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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.

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To use this module NCBI-blast+ has to be installed.


Create Blast-Database

This module can create blast databases from the sequences in a T-ACE database. It is possible to create blast database from the contig, protein or read sequences. The created will be named like the corresponding T-ACE database, if the proteins are used a '_prot' will be appended to the name. If the reads are used a '_reads' is appended.

To use this module NCBI-blast+ has to be installed.

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NCBI-Blast

This module can blast contig sequences from a T-ACE database against any blast database available at NCBI. It sends the query sequence directly to the NCBI web-blast and writes the results into the database.
The 'Run blast for'-combobox allows to select a subset of sequences from the T-ACE database for blasting at NCBI. The option 'selected sequences' refer to all sequences in the 'Database browser'-table or a project tab table, which have 'checked'-status in the first column.

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Run compare

'Run compare' is used to compare multiple subsets of contigs against the contigs of all subsets. After opening 'Run compare' new 'Run'-cohorts can be added through the 'Cohort manager'-tab. The columns 'cohort' and 'runs' can be modified by clicking on a cell. In this way the cohort name can be changed or runs can be added or removed from a cohort. Press the 'Save'-button to adopt those changes. When all cohorts are added, it is necessary to press the 'Update'-button in the lower right corner of the tab.

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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.

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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.

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