Pairwise and multiple sequence alignment can be performed pre and post analysis. Alignment can be performed using the Align operation under the Post-processing tab. We currently support the iteration-based alignment method, MUSCLE (multiple sequence comparison by log-expectation) for sequence alignment.
To perform sequence alignment, select two or more sequences and click Post-processing followed by Align. Depending on your sequence type, set your sequence type by selecting either Nucleotide (DNA and RNA) or Protein (amino acid).
You can choose to either align the whole sequence or just the CDS region of your sequences. To align the entire sequence, click Entire sequence under Region to align. This operation will align all the selected sequences from the 5' end to the 3' end.
To align the CDS regions only, click Extract CDS with name and select the appropriate CDS name in the drop-down. This operation can only be performed on sequences consisting of CDS annotations and the CDS annotation will be automatically picked up and added to the dropdown. This operation will align the sequences from the 5' end to the 3' end of the CDS annotation.
In the absence of CDS annotations within the selected sequences, you will see the following message:
You can also align translated sequences by selecting the Translate nucleotide sequence(s) prior to alignment option. Set the appropriate genetic code and translation frame. This operation will translate the nucleotide sequence according to the selected genetic code and translation frame before aligning the sequences.
Click Run to start the operation. This operation will output an alignment file to the same experiment folder where the sequences used for the alignment are located.