3.2.15 Contig Assembly a.k.a Sequence Alignment
Details about this feature can be found in the main Genome Compiler user guide:
See section 1.24 for Sequence Alignment.
To open Contig Assembly in Vector NTI you should either choose “Assemble”- “ContigExpress” in the main menu (Figure 184.108.40.206) or click on Assemble Chromatogram Data icon in the Quick Start page and select Contig Express from the suboptions (Figure 220.127.116.11). Alternatively, open the Start menu and select “Start”-“Programs”-“Invitrogen”-“Vector NTI Advance”-“ContigExpress”.
ContigExpress uses CAP3 to drive the assembly process.
Genome Compiler allows you to perform multiple pairwise sequence alignments, including alignments with chromatogram files. The sequence alignment algorithm used is ClustalW.
Step 1 - Load Template Sequence.
- In order to align sequences, it is first necessary to open the project in Genome Compiler which contains the template sequence.
Step 2 - Opening the Alignment Settings Dialog.
- You need to open the Alignment Settings Dialog (Figure 18.104.22.168) in order to upload your alignment files. This Settings dialog can be accessed either from the menu bar, by selecting "Tools“-"QC Alignment“ (Figure 22.214.171.124) or from the Annotation Layers menu at the bottom right panel of the opened project by selecting the "QC alignment" settings icon (Figure 126.96.36.199) or by selecting the "Align" icon in the main toolbar (Figure 188.8.131.52).
Step 3 - Uploading Sequences to Align.
You can upload as many sequences to align as you like, whether they are in overlapping regions or on opposite ends of the sequence. You can either: Drag and drop a file from the Materials box or "Choose a file" (.AB1, .SCF, text, fasta/multisequence fasta, genebank) from your computer or simply type/paste a raw DNA sequence, enter a name and select "Add“ (Figure 184.108.40.206). The files will be added to the "Selected Sequences" list.
Notice that for viewing chromatographs you must upload the .AB1 files from the “QC Settings” dialog.
For further details regarding the sequence alignment please refer to section 1.24.