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Pseudomonas Genome Database - Sequence updates

Important change: Ability to update nucleotide sequence implemented (2004-01-14)

Please note that we have now implemented the ability to update the sequence, not just the annotation, of the Pseudomonas aeruginosa PAO1 genome sequence. This has a notable impact on many annotations, since of course any insertions and deletions in the sequence result in a change of the base pair coordinate numbers for all genes downstream of the sequence insertion/deletion. We will therefore note these in the log file of updates with a special notation "SEQUENCE UPDATED:" at the beginning of the log file description of the change. To find all such changes in the database, please search, using the database search tool, or log file search tool, for the term "Sequence Updated". Your search will return all occurrences of any sequence updates.

As discussed at the Pseudomonas 2003 conference forum on this topic, such updates mean that coordinates of genes should not be used to identify them, since such coordinates may change when nucleotide updates are made. Therefore, PLEASE USE PA NUMBERS AS YOUR PRIMARY IDENTIFIER FOR IDENTIFYING ANY GENE FROM THIS GENOME, since both the gene bp coordinates and gene name annotation may change over time. Note that the only rare exception where PA number may change is when two genes are merged into one (i.e. we realize that two open reading frames that we thought were two genes are actually just one gene, after correcting a frame shift error or equivalent). In such cases, one of the two PA numbers will be used for the merged gene, and the other PA number retired, never to be used again. If the retired PA number though is ever searched for in the database it will automatically forward the request to the record for the merged gene. For example, if PA1000 and PA1001 were merged, PA1000 would become the PA number of the new merged gene, and any queries involving PA1001 would automatically forward to the record for PA1000. Thus, in such cases PA number will still represent a suitable unique identifier for a given gene in the P. aeruginosa PAO1 genome, even for such rare cases.

If you have any questions or comments about this change and its implementation, don't hesitate to contact us!