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Sequence related tools
 Export sequences without gaps
From a comparison containing a sequence type experiment, aligned or unaligned sequences are exported without gaps in a tab-delimited text format. The script pops up a dialog box that asks to select the database field(s) you want to export (you can choose more than one field) and the sequence type.
Export sequences in FASTA format
Allows sequences from selected entries in the database to be exported in FASTA format. From the menu the script pops up, you can choose the sequence type, and the fields to export.
Translate selected sequences
From a selected set of entries, the script will translate the nucleotide sequences into amino acid sequences. The script first creates a file AMINOTRANS.TXT
in the BioNumerics startup directory, which contains all known translation tables. It then pops up a dialog box whhere you can select a sequence type to translate
and a translation table to use. When finished, the script has created a new Sequence type, which has the same name as the translated Sequence type,
with an extension _TRANSL. This new Sequence type contains the translated sequences for the selected entries.
The script has also created a new database field, TranslationFrames, wherein the translation frame can be specified for each entry and per Sequence type.
Setting the frames happens through another script Set reading frame described below.
Note: This script installs itself as a menu item Sequence > Translate selected sequences when copied to the local BioNumerics script folder.
Set reading frame
Using this script, the reading frame can be set for a particula entry, and a particular sequence type. This script only works for nucleic adic Sequence types
which have been translated into amino acid sequences using the script Translate selected sequences which is described above.
The script should not be run directly from the website, but should be installed locally instead by pressing the  in the button toolbar of this window!
When installed, it appears in the Entry edit window as a menu Sequence > Set frames.
When running the script it pops up a dialog box where you can select a translation table (installed by the script Translate selected sequences which is described above). You can also specify a translation frame for each Sequence type separately. To effectively carry out the translation, press the <Translate> button and press <OK> in the translation report that appears. The script fills a field TranslationFrames with the frame specified for each Sequence type that has an associated translated Sequence type.
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