How to Perform and Analyze a Sequence Alignment

Biochemistry, Molecular Biology, and Cell Biology Protocols >> How to Perform and Analyze a Sequence Alignment

1. Obtain the nucleic acid or amino acid sequence from NCBI in FASTA format.
2. Enter the sequences obtained into a program such as ClustalW or Blast.
3. Sequences in areas with a high degree of conservation indicate that they are likely important for function or structure. Conservation can mean having basic residues the same (eg Lysines, Arginines) or acidic residues the same (eg Glutamate, Aspartate), or having a similar side chain size (eg Cysteine, Serine)
4. Sequences in areas with a low degree of conservation indicate that they may be important for variability and specificity.
5. One set of sequences important to align would be the DNA or protein sequences of the same molecule in different species. Another would be to align the same family members of a particular domain.