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The Edit menu


Add sequences
Edit DB
Invert selection
Remove selected sequences
Save
Show

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Add sequences

With 'Add sequences' it is possible to add the checked entries from the 'Database browser', 'Sequence browser', 'Blast'-tab or a project tab to a project tab. After clicking on 'Add sequences' a list of all available project tabs will appear.

Edit DB

'Edit DB' contains a lot of options to modify and update a database.

Add ACE file
Add blast results
Add InterProScan results
Add nucleotide file
Add protein file
Add SAM file
Change comment
Create database copy
Delete selected contigs
Delete selected hits
New nucleotide sequence
Update
Update blast2interpro entries
Update coverage
Update database info
Update descriptions
Update domain2interpro entries
Update GO-Statistic
Update KEGG-Maps
Update read distribution
Update read status
Update sequence entries

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Add ACE file
This option loads the contents of an ACE file into the database. The read mapping information for each contig of the ACE file will be available.

Add blast results
It adds the blast hits from a tabular tab-delimited blast output file (-outfmt 6) to the database. Take care to choose the right blast reference table from the 'Database identifier'-combobox, otherwise the references for the blast hits will not be available.
After adding the hits 'Update sequence entries' and 'Update descriptions' should be performed.

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Add InterProScan results
It adds the domain, InterPro and GO hits to the database. As input file serves a results file of InterProScan in the .raw format.

Add nucleotide file
The option adds the sequences from a fasta file as contigs to the database.

Add protein file
The option adds protein sequences from a fasta file as proteins to the database. As input serves a protein file from InterProScan in the .input format.

Add SAM file
This option loads the contents of a SAM file into the database. The read mapping information for each contig of the SAM file will be available. Before the SAM file is uploaded the reference contigs must be imported into the database, otherwise the reads in the SAM file cannot be assigned. The upload of SAM file will take a considerable amount of time. Have also in mind that T-ACE is not designed as a genome browser, but for de-novo transcriptomes. This means contig sequences should not be much longer than 60.000 bp and should not contain over 100.000 reads (at least if those reads shall be displayed).

Change comment
This changes the database comment.

Create database copy
Creates a copy of the complete database.

Delete selected contigs
Deletes the checked contigs and all its proteins and hits from the database.

Delete selected hits
Deletes the checked hits of the 'Blast results'-tab, 'InterProScan results'-tab, 'GO hits'-tab or 'KEGG'-tab from the database, depending on which tab is raised.

New nucleotide sequence
With 'New nucleotide sequence' a new contig sequence can be added to the database. The 'Header'-field sets the name for the new contig and the 'Sequence'-field the sequence. With the 'Add comment'-field a comment can be added to the new contig. The radio buttons display the open reading frames (ORFs) of the different frames of the sequence. The ORFs are displayed in yellow, while start codons are green and stop codons are red.

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Update

Update blast2interpro entries
This option tries to associate the blast hits of a contig with InterPro hits, if there are associated InterPro hits they will be added to the contig annotation. The blast2interpro associations can be found in the 'interpro2protein'-table of the 'refdb'-schema of the parent database.

Update coverage
This function calculates the average contig coverage, it is only necessary after adding contig sequences with read mapping information, for example after adding an ACE file. The coverage is needed for the 'Coverage'-functions of the 'Database statistics'-tab.

Update database info
It updates all the information shown in the 'Database info'-tab.

Update descriptions
Updates the standard descriptions of all contigs, which is shown in the description column of the 'Database browser'-tab. It necessary to update the descriptions after adding new annotations over 'Add blast results' or 'Add InterProScan results'.

Update domain2interpro entries
This option tries to associate the domain hits of a contig with InterPro hits and GO terms, if there are associated InterPro hits they will be added to the contig annotation. The domain2interpro associations can be found in the 'interpro2domain'-table of the 'refdb'-schema of the parent database.

Update GO-Statistic
Updates the GO-tree of the 'GO statistics'-tab. It is necessary to update the GO-tree after adding new GO hits to the database.

Update KEGG-Maps
This option tries to associate the blast hits of a contig with KEGG ontologies and adds them to the contig annotation. Then all KEGG hits will be reviewed for updating the 'KEGG maps'-table.

Update read distribution
Updates the affiliation of the reads to the different sequencing runs contained in the database, for each contig. This update should be run after adding sequences and/or sequencing runs to the database, otherwise features like 'Stress vs. Control' or 'Mapping' will not work correctly.

Update read status
This option checks if a read in the database is associated with a contig or if it is a singleton. This is only necessary after adding new read sequences, or contigs with read mapping information to the database.

Update sequence entries
Updates the annotation status of all contigs. It counts the number of hits for the different annotation categories. It necessary to update the sequence entries after adding new annotations over 'Add blast results' or 'Add InterProScan results'.


Invert selection

Inverts the checked status of a table in the upper half of T-ACE, depending on which tab is raised.

Remove selected sequences

Removes the checked rows from a project tab table.

Save

It saves the 'selected blast results', 'selected hits' or 'selected sequences', depending on which option is chosen.

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selected blast results
To use this option the 'Blast'-tab has to be raised. It writes the information of all checked rows in the results table of the 'Blast'-tab into a tab-delimited text file.

selected hits
This option writes the information of all checked rows in the hit table of the 'Blast results'-tab, 'InterProScan results'-tab or 'Go hits'-tab, depending on which tab is raised, into a tab-delimited text file.

selected sequences
This option writes the contig sequences of all checked rows of the 'Database browser', the 'Blast'-tab or a project tab into a fasta file, depending on which tab is raised.

Show

The 'Show'-option does the same as the 'Save'-option, with the difference of displaying the information in a window before saving.


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