How to Perform and Analyze a Sequence Alignment

  1. Get the nucleic acid or amino acid from NCBI in FASTA format.
  2. Enter the sequences obtained in programs such as CLUSTALW or explosion.
  3. The order in areas with a high degree of conservation suggests that they tend to be important for the function or structure. Conservation could mean having the same basic residues (eg lysines, Arginines) or the same acid residue (eg, glutamate, aspartate), or have the same size of the side chains (such as cysteine, Serine)
  4. The order in areas with a low level of conservation suggests that they may be important for the variability and specificity.
  5. A set of sequences will be important to align the DNA or protein sequence of the same molecule in different species. Another would be to align the same family members of a particular domain.