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T-ACE DB Manager

This script creates the 'parent database', which will contain all databases created with T-ACE as schemata. It also creates the reference schema, which holds most of the annotation information, such as domain descriptions.
If InterProScan shall be used on the postgresql server, a copy of this script needs to be located on the server, otherwise InterProScan will not be available.

Just execute the script to open the GUI or use '-h' for help about the command line usage.

Database connection
Database options
Reference database
User management

Database connection

The 'Database connection'-tab, sets all needed parameters to establish a connection to the chosen parent database. For all operations in the 'Reference database'-tab or 'User management'-tab it is necessary to login as a superuser.
It is not necessary to press the 'Run'-button to set the database connection.

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Database options

The 'Database options'-tab allows the creation/deletion of databases. It is also possible to fill databases with sequences and annotations, but it is easier to do all this directly with T-ACE.

Database name
Sets the database schema that shall be modified.

Create database
Creates a new database with the name set in the 'Database name' entry field.

Delete database
Deletes the database with the name set in the 'Database name' entry field.

Add ACE file
Adds the contents (contig and read information) of a ACE file to the selected database. The contig names in the database will consist of the database name and the contig name from the ACE file.

Add nucleotide sequences
Adds the sequences from a fasta file to the selected database as contigs.

Add protein sequences
Adds the sequences from a fasta file to the selected database as proteins. For this an InterProScan protein input file should be used. If a sequence from the file does not have a corresponding contig in the database it will be omitted.

Add read sequences
Adds the sequences from a fasta file to the selected database as reads with the given run id.

Add blast results
Adds the blast hits from a blast output file, in table format, to the selected database. If a blast hit has no corresponding contig in the database it is omitted.

Add InterProScan results
Adds the InterProScan results from an InterProScan output file, in raw format, to the selected database. If a domain hit has no corresponding protein sequence in the database it is omitted.

Blast2InterPro
Searches the 'protein2interpro' reference table for InterPro hits associated with blast hits of the selected database. The InterPro hits, and the corresponding GO terms, are added to the annotations of the selected database.
The 'Blast2InterPro'-function is also available from T-ACE.

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Reference database

The 'Reference database'-tab allows the creation of the parent database, functions and reference schema. To fill the different tables of the reference database, various data files are needed. In most cases, the download source of the needed file is shown beneath the corresponding option. Some of the files have to be unpacked before they can be used as input.

It is possible, to start working with the Transcriptome Viewer after the execution of steps 1 and 2. The other steps are more or less optional, depending on the requirements for the sequence annotation.

1. Create parent database
This creates a parent database accordant to the parameters set under 'Database connection'.
It is necessary, to set the path to the 'T-ACE_DB_Manager.tcl' and the InterProScan folder on the postgresql server, if InterProScan shall be used.

2. Create functions
Creates the functions schema of the parent database. The functions are necessary for many T-ACE features. Through the 'User management'-tab the function right for each user can be set.

3. Add GO references
Writes the gene ontology terms from an obo file to the GO reference table.
The reference can be downloaded at:

4. Build GO-tree
Creates a GO-tree from the GO references. The tree is necessary for the 'GO statistics'-tab of T-ACE.

5. Add Gene3d references
Adds the gene3d domain entries from a file to the gene3d reference table.
The reference file can be downloaded at:

6. Add SMART references
Adds the SMART domain entries from a file to the SMART reference table.
The reference file can be downloaded at:

7. Add KEGG references
Adds the KEGG ontology terms from a file to the KEGG reference table.
The reference file can be downloaded at:

8. Add KEGG Map references
Adds the KEGG pathways from two files to the KEGG Maps reference table.
The reference files can be downloaded at:

9. Add InterPro2GO references
Adds InterPro2GO links to the interpro2go reference table.
The reference file can be downloaded at:
or

10. Add Protein2InterPro references
Adds Protein2InterPro links to the protein2interpro reference table.
The reference file can be downloaded at:

11. Add Protein2KEGG references
Adds Protein2KEGG links to the protein2interpro reference table.
The reference files can be downloaded at:
and

12. Add blast references
Creates a blast reference table accordant to the given 'database identifier', e.g. nr, nt, uniref100, uniprot_sprot. The references from the file will be written to the created reference table.
The reference file needs to be in a special format. It should be tab-delimited and has to contain the following columns:
A reference file can be downloaded at:

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User management

The 'User management'-tab allows the creation/deletion of user accounts for the postgresql databases. Also access rights to functions and individual databases can be given or denied.
If a new user is added the password for the account will be the same as the user name. Before a user can be deleted all his databases have to be removed, otherwise the user will only loose his access rights.

Add new user
This function creates a new user for the postgresql parent database. The name of the new user is set in the 'User name' entry field. The checkbutton 'cDB' allows the new user to create schemata in the parent database.

Grant function rights to user
This function grants execution rights to functions of the function schema to a new user. To which functions rights are granted depends on the radiobutton setting:

Grant access rights to user on database
This function grants access rights for the given database to the user. The user may also have write access if the accordant checkbutton is selected.

Delete user
Deletes the user login role, if no database object depends on it. If the user cannot be deletes the user just looses all access rights to the parent database.

Revoke function rights of user
Revokes the execution rights of all functions from the user.

Revoke access rights of user on database
Revokes all access rights to the given database from the user.

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