Master Oligo Box

Oligos that you create in DNADynamo are saved in the 'Master Oligo Box'

When you open a DNADynamo features map, oligos stored in the 'Master Oligo Box' that potentially anneal to the template DNA that the features map represents are displayed on the features map

You can open the Master Oligo Box using menu option 'Boxes' -> 'Master Oligo Box'

You can select oligos listed in the 'Master Oligo Box' and then delete, edit or locate, or export them

You can also edit oligo names and comments directly within the Master Oligo Box display area

Oligo Box Store File Location and 'Manage-Store' options

By default DNADynamo stores oligos in a file called AllOligosBox.CBY in your DNADynamo installation folder. You can open the installation folder using menu option 'Help' -> 'Open Installation Folder'.

You can use the 'Manage Store' menu options to create additional/alternative store files for your Master Oligo Box.

First create a 'masteroligobox' store file in an alternative file location, or copy your default AllOligosBox.CBY file to another file location, then use "Select a 'masteroligobox' store file to use" to point to the new file.

Note that if you choose to share a store file with other DNADynamo users by placing the file in a 'Cloud' folder such as 'DropBox' or 'SkyDrive' etc and two users edit the master oligo box simultaneously - your cloud folder may produce two versions of the file - one of which is referred to as the conflicted copy.

If you use DropBox or Skydrive - DNADynamo tries to automatically detect the presence of 'conflict' files - and prompts you to resolve them

If you use an alternative cloud storage provider or a version of dropbox or skydrive which produces conflict files in a format not recognised by DNADynamo, you can use the "Compare to another 'masteroligobox' file to find and optionally resolve differences/conflicts" menu option Email us if you use cloud option that produces conflict files in a format not recognised by DNADynamo - and we'll try and add the format to an update

Importing Oligos into the 'Master Oligo Box'

You can import oligos into the Master Oligo Box from a text file in FASTA format, or comma/space tab line separated formats, from another DNADynamo oligobox.cby file, or from an NTI database or oligo archive file

note that spread sheets often have options to output tabulated data in CSV format

example of fasta format (comments not supported)

>JS5
GGATCCTTACTATCATCTATA
>JS6
GAATTCTACGTACGTACGTACGTTACG
>JS7
ATCGCTAGTACGTACGTACGTCGAT


example of comma separated values (CSV) format without comments - note that each oligo must be on a separate line

JS5, GGATCCTTACTATCATCTATA
JS6, GAATTCTACGTACGTACGTACGTTACG
JS7, ATCGCTAGTACGTACGTACGTCGAT


example of comma separated values format with comments - note that each oligo must be on a separate line

JS5, GGATCCTTACTATCATCTATA, oligo with BamH1 site
JS6, GAATTCTACGTACGTACGTACGTTACG, oligo with EcoRI site
JS7, ATCGCTAGTACGTACGTACGTCGAT, new sequencing oligo


example of space/tab separated format with comments - note that each oligo must be on a separate line

JS5 GGATCCTTACTATCATCTATA oligo with BamH1 site
JS6 GAATTCTACGTACGTACGTACGTTACG oligo with EcoRI site
JS7 ATCGCTAGTACGTACGTACGTCGAT new sequencing oligo