MSA - Procedure

1. Selecting DNA or protein sequences:

Aligning protein sequences is the better choice because protein sequences are three times shorter than the corresponding DNA sequences, and protein sequences use a more informative alphabet of twenty amino acids in contrast to only four nucleotides in DNA sequences. The protein or DNA sequences to be input into the program need to be converted to appropriate formats for an automatic multiple sequence alignment program such as ClustalX. Sequence formats are simply the way in which the amino acid or DNA sequence is recorded in a computer file.

The FASTA sequence format is a widely accepted format. It starts with the greater than symbol (>), gene identification number, its reference protein accession number, and its name followed by the sequence.