At present, most computational methods (49) and databases (21) are based on the assumption that a single isoform represents each gene. The SwissProt database, for example, combines all variants of the same gene in a single entry. These entries include experimental data and predictions, which are widely referenced from a number of external sources. One of the sequences in each entry, almost always the longest, is designated as the display sequence and the remaining sequences are included as splice variants. External databases and methods that use SwissProt as their standard often ignore these alternative sequences. If databases are going to condense gene products from the same gene into a single entry for technical reasons, it is better that the sequence that ‘represents’ the gene is the APPRIS principal isoform.
