Automatic end trimming

Using its revolutionary Trimming Engine, DNA Baser automatically detects and trims the untrusted regions from your samples!
This happens whenever it imports a sample from disk. Therefore, all samples that you open in DNA Baser for sequence assembly, conversion, vector removal, editing, etc have the untrusted regions already removed! No more manual editing, no more wasted time!

These regions appear in the CHROMATOGRAM VIEWER window highlighted in gray color as shown in the figure below:

Fig 1 - Untrusted region of bases highlighted in gray color.

Important:

The untrusted regions are not actually deleted from your sample. They are rather ignored.

How the Automatic Trimming Engine works

The bases are removed according to the Trimming Engine parameters. Bases located at the ends of the chromatogram with confidence scores lower than a user defined threshold are grouped together and marked as untrusted. When the sample is used (assembled to contig, batch processed, edited) these regions are simple ignored.

Samples that are suitable for automatic ends trimming

The detection of untrusted regions is based on the confidence scores (confidence score) assigned to each base. Therefore, DNA Baser will remove the untrusted regions only from chromatograms that include the confidence score information. Most ABI files and all SCF files have this information included. Plain text samples (such as FASTA) cannot store this information.

Does it really cuts the bases away from my samples?

DNA Sequence Assembler automatically detects the untrusted regions in chromatograms before starting the assembly process. It doesn't really cut away the bases, it just marks them as untrusted so they won’t be taken into consideration when the assembly process starts. Your original files will remain untouched!

How can I clean untrusted (low quality) regions?

You don't have to manually cut the low quality ends of your samples. DNA Sequence Assembler and Chromatogram Explorer will automatically do it for you. Both programs use the same Trimming Engine. By altering the parameters of the Trimming Engine you can control how much you want to cut from your samples

Note: Chromatogram Explorer will not allow you to edit the bases of your chromatograms. However, DNA Baser allows you to do that.

In my sample, I want to manually define low quality regions and save them to disk.

You can manually mark bases as untrusted, but the information about untrusted regions cannot be saved to disk. Simply put, the FASTA, ABI, SCF format does not support this. “Gray regions” (untrusted bases) is a unique feature offered by DNA Baser! The regions are gray only inside DNA Baser. Once you close DNA Baser, this information is lost. The program re-detects untrusted regions next time you reload that sample by reapplying the trimming engine algorithm.

When saving your samples back to disk in ABI/SCF format, the only way to keep your sequence trimmed after saving them to disk is to actually delete the gray (low quality) regions. To do this, please follow these steps:

1. Load your sample(s).
2. Manually delete the low quality regions by selecting the bases you want to delete, then pressing the Delete key. In most cases, DNA Baser will automatically detect and mark in gray color the low quality ends you may want to delete.
3. When done, save your sample back to disk: in the File menu, choose 'Save sample as...', then choose 'SCF' if you want to keep your chromatogram (recommended) or FASTA.

Why my are alignments wrong? 

The problem with wrong alignments often appears when the untrusted regions of the chromatograms are poor and they have not been properly cleaned. DNA Sequence Assembler is doing the trimming automatically if the sample stores confidence score information. If not, the user should manually cut the untrusted regions.

Fig 1 - A chromatogram showing untrusted region (gray) and confidence scores (vertical green bars above each base).

Automatic trimming engine in action - Video tutorial

How can the automatically trimming engine save time by eliminating all ambiguity manual corrections. Please note that there are 381 ambiguities i the trimming engine is no used. After automatically cleaning the low quality ends, there are only 12 ambiguities!!
Click here to enlarge the video.

Index

• Manual end trimming
• What is a chromatogram?
• What is a good chromatogram?
• FAQ about confidence scores (confidence score)
• Untrusted regions