Final answer:
Using predicted protein sequences from RefSeq for protein sequence alignment is a valid approach, but it has limitations and should be validated with experimental data. Caution should be exercised due to potential inaccuracies and the absence of certain protein features like isoforms or post-translational modifications.
Step-by-step explanation:
Using predicted protein sequences from RefSeq for protein sequence alignment can be a valid approach, but it has some limitations. RefSeq provides a curated collection of reference sequences, which are derived from a combination of experimental and computational data. Predicted protein sequences from RefSeq are generated using computational methods based on gene prediction algorithms. While these predictions are generally accurate, they may contain errors or inaccuracies. It is important to be cautious when using predicted sequences and to validate them with experimental data if possible.
One example of a potential issue with predicted protein sequences is the presence of frameshifts or incorrect gene predictions, which can result in inaccuracies in the alignment. Additionally, predicted sequences may not include all possible isoforms or post-translational modifications that can affect protein function. It is always recommended to use experimentally verified protein sequences whenever possible for more reliable results.