Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al

In their paper “Database verification studies of SWISSPROT and GenBank” Karp et al. (2001) conclude: (1) “SWISS-PROT is more incomplete than we expected. . . ”; (2) “Even if we combine SWISS-PROT and TrEMBL, some sequences from the full genomes are missing from the combined dataset”; (3) “In many cases, translated GenBank genes do not exactly match the corresponding SWISS-PROT sequences, . . . ”; and (4) “. . . that SWISS-PROT does not identify a significant number of experimentally characterized proteins”. These results, and the approach used to arrive at these results, are in our opinion somewhat misleading. Herein, we only focus on four major points. First, there has never been a claim that SWISS-PROT is comprehensive. Thus, it is surprising that Karp et al. found that “SWISS-PROT is more incomplete than we expected. . . ”. To make sequences available as quickly as possible without diluting the quality of SWISS-PROT, the supplemental database TrEMBL was introduced in 1996 and contains the translation of all coding sequences (CDS) in the DDBJ/EMBL/GenBank nucleotide sequence database, except those already included in SWISS-PROT. Snapshots of the SWISS-PROT, TrEMBL and TrEMBLnew databases are released weekly, synchronised with the DDBJ/EMBL/GenBank nucleotide sequence database and provide comprehensive coverage (ftp://ftp.ebi.ac.uk/pub/databases/sp tr nrdb/). The weekly comprehensive SWISS-PROT/TrEMBL nonredundant database (SPTR) has been widely publicised on the EBI and ExPASy web-servers and in various publications (e.g. Apweiler, 2000). Second, the authors’ assertions that “Even if we combine SWISS-PROT and TrEMBL, some sequences from the full genomes are missing from the combined dataset.” and “SWISS-PROT curators apparently chose not to replace existing SWISS-PROT sequences with sequences from complete-genome projects” are rather inaccurate. Karp et al. tried to establish corresponding sets of SWISS-PROT/TrEMBL proteins and