3.3.9 Sequence Alignment
Details about this feature can be found in the main Genome Compiler user guide:
See section 1.24 for Sequence Alignment.
In ApE in order to align sequences you should first open all the files and choose the reference sequence as well as the “Align to Windows” in the “Align DNA” dialog. This dialog can be launched through the main tool bar (Figure 188.8.131.52) or from the main menu by choosing “Tools”- “Align Sequences” (Figure 184.108.40.206).
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 220.127.116.11) in order to upload your alignment files. This Settings dialog can be accessed either from the menu bar, by selecting "Tools“-"QC Alignment“ (Figure 18.104.22.168) or from the Annotation Layers menu at the bottom right panel of the opened project by selecting the "QC alignment" settings icon (Figure 22.214.171.124) or by selecting the "Align" icon in the main toolbar (Figure 126.96.36.199).
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 188.8.131.52). 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 1.23.