The Project Builder

The Project Builder is the place where you define your current project. The project is the set of files on which tasks (such as sequence assembly, batch sequence processing) are applied. The Project Builder it is only used to build a new project. This page explains how to load an existing project or to save the current project.

The Project Builder has the following components:

• Tasks pane
• Sample Explorer
• Job List
• Assemble to reference
• Metadata Integrator

The Tasks pane

The following assembly tasks can be performed:

Start SINGLE CONTIG ASSEMBLY
Start BACTH CONTIG ASSEMBLY - BASED ON NAME PATTERN
Start BATCH CONTIG ASSEMBLY - BASED ON SUBFOLDERS
Start BATCH SEQUENCE PROCESSING

The Sample Explorer

You can use the Sample Explorer to quickly open and inspect your samples. The FOLDER LIST (the left side of the Sample Explorer) enables navigation through folders, while the FILE LIST (the right side of the Sample Explorer) shows the content of the folders. The FILE LIST will display all file types or only certain types of files. The choice is made from the FILE TYPE box.

Supported files

DNA Sequence Assembler supports multiple file formats. You can make the Sample Explorer to show all suppported files or only a specific type (for example only chromatogram files).

The Job List

The JOB LIST contains the files on which the desired type of function (either sequence assembly, batch sequence assembly, sequence processing) will be applied. To add files from the FILE LIST to the JOB LIST you can use the add buttons or drag and drop files from Sample Explorer or from Windows Explorer. Different file types (SCF, ABI, FASTA, SEQ, etc) can be mixed (assembled) together.

Adding samples from Sample Explorer to the Job List

Removing samples from Job List

 

Add only selected files from the FILE LIST to the JOB LIST
Add all files from the FILE LIST to the JOB LIST

Delete only selected files from the JOB LIST
Delete all files from the JOB LIST

The Project Name panel

Project path

By default, DNA Baser automatically chooses a path (see figure above) where to output the project file and the contig file. By default, the path is the current folder opened in Sample Explorer. This path dynamicaly updates as you navigate through your folders AS LONG as you don't manually edit it. Once you type something into the 'Path' edit box, the program will consider that you want to keep that path and it will not automatically update it (unless you start building the next project). IMPORTANT: Please make sure that DNA Baser has write permissions to the output folder.

Project name

The name of the project is also choosen by DN Baser automatically based on the name of the current folder opened in Sample Explorer.

The contig will be saved under a similar name.

The Assemble To Reference panel

If checked, the assembly process will be done to a reference sequence. To define a reference, drag and drop it from Sample Explorer into the 'Reference' box. For more details about assembling to reference, click here.

The Metadata Integration panel

If checked, the corresponding metadata will be added to all sequences that result from all the sequence assembly functions or from the sequence processing function. For more information regarding metadata, click here.

Other functions/tools

Show the content of the desktop in the FOLDER LIST and FILE LIST.
Show the content of My documents the FOLDER LIST and FILE LIST .
Refresh the FOLDER LIST and FILE LIST .

Quick access to the sequence assembly options.
Open online help for sequence assembly.
Go to output folder (the folder where the result of the last task was saved)