DNASTAR

How does SeqMan Pro calculate the consensus sequence?

DNASTAR’s DNA sequence assembly software, SeqMan Pro, uses a proprietary “Trace Evidence” algorithm that has significantly better consensus calling accuracy than the “Majority” method used by most consensus calling programs.

How do I get best possible results in my de novo Sanger assembly?

De novo assembly is sensitive to low quality or untrimmed vector sequences. SeqMan Pro is a sequence assembly tool that provides fast and accurate trimming options based on quality and vector (or other contaminant) sequences.

Can I assemble multiple samples for variant analysis?

SeqMan provides an “Assembly in Groups” feature that identifies the unique characters in the trace file names so that they can be grouped together automatically as “samples”.

Can I edit a de novo assembly made with SeqMan Pro?

Yes. De novo assembly produces a fully editable SeqMan project file (.sqd) where base-level and contig-level editing can be carried out.

What file types can I import to assemble in SeqMan Pro?

SeqMan Pro accepts output from most Lasergene applications as well as 454, ABI, ALX, FASTA, GCG, GenBank, Phred, SCF, Sequencher, .eff, .fof, .txt and .zip files. For a complete list, see our File Formats page.

Can I annotate my consensus sequence?

Yes, there are several ways you can add features to your consensus sequence:

• Copy features from constituent sequences to the consensus
• Collect features from a BLAST search
• Manually add a feature to a selected range of sequence

When should I assemble sequences using a reference?

A known sequence can be used as a backbone/template/reference sequence upon which to build your sequence assembly. This lets you perform the assembly with lower average sequence coverage, thus saving a substantial amount of sequencing effort. Simply add the reference sequence to SeqMan Pro along with the other sequences. Select it and press the Mark Ref button to mark it as the reference sequence. If no reference sequence is available for your organism, try using one from a closely-related organism.

Can I add new data to my assembly?

Yes, you can add new sequences and include them in a finished assembly. After performing an assembly in SeqMan Pro, use a Sequence > Add command and add additional sequences. Press Assemble. The new sequences and old sequences will be reassembled as a group.

How can I organize or join multiple contigs in my assembly?

Try relaxing some of the assembly parameters such as Match size or Minimum match percentage. Then run the assembly again to see if the contigs will merge together organically. Alternatively, force-join contigs at their termini by selecting the contigs to join and choosing Contig > Force Join Contigs.

How do I separate contigs at regions of sequence conflicts?

In the Alignment View, use Edit > Find and select Conflict Split as the search type. If you find a high-conflict region where you wish to separate the contig into two contigs, select Contig > Suggest Conflict Splits.

How can I export my completed sequence assembly?

After using our DNA assembly software, SeqMan Pro, to create an assembly, select Contig > Save Consensus and choose from the following options:

• Single File – all selected contigs are saved in a single file.
• Multiple Files – each selected contig is saved as a separate file.
• As Single Sequence – all selected contigs are joined end-to-end in the same order in which they appear in the Project Summary and saved as a single sequence in one file.
• One Sequence Per Scaffold –contigs for a given scaffold become a single sequence by being joined end-to-end in the same order in which they appear in the Project Summary.

How can I use SeqMan Pro as a DNA chromatogram viewer?

In the Alignment view, click the triangle to the left of a sequence name to display its chromatogram. Chromatograms are available only for ABI sequences.