12 Multiple sequence alignment

Performing multiple sequence alignment analysis (based on mafft) and generating sequence conservation profiles.

12.1 Sequences based multiple sequence alignment

  1. Essential parameters: Only Input data type, Gene IDs/Sequences, and Sequence type are needed for basic usages.
  2. Advanced parameters: 5 other parameters for controlling MAFFT alignments are supplied with detailed explanations.

Simply, users just need to select each parameter sequentially as labeled in the figure (or simply just click the Demo1, and Demo2 buttons).

A screenshot of the one type of selection for Multiple Sequence Alignment.

Figure 12.1: A screenshot of the one type of selection for Multiple Sequence Alignment.

Clicking Submit, after several seconds, the multiple sequence alignment result would be listed below.

Multiple sequence alignment results. One can enlarge the number to alignment length to display all amino acids in one line.

Figure 12.2: Multiple sequence alignment results. One can enlarge the number to alignment length to display all amino acids in one line.

12.2 Gene/Transcript IDs based multiple sequence alignment

12.3 Reference

  1. Rozewicki, Li, Amada, Standley, Katoh 2019 (Nucleic Acids Research 47:W5-W10) New! MAFFT-DASH: integrated protein sequence and structural alignment