Comparison of Status of Functional Genomics
| Functional genomics | Sequence analysis/structural genomics | |
| Databases | flat files or databases developed by individual researchers for each study. Centrally managed databases in initial development.[ii] | centraly managed, global sequence databases used by entire research communities |
| “Straw man” database standards proposed (Bassett et al. 1999) | databases and standards established; e.g., GenBank, PDB, SwissProt (Bernstein et al. 1977;Bairoch and Apweiler 1999; Benson et al. 1999) | |
| Data standards | no uniform standards for data reporting (Bassett et al. 1999) | uniform standards for sequence and structure submission, partially or completely automated (e.g., BankIt for GenBank, ADIT for PDB) |
| different data reported by different methodologies (see text) | reported sequence data independent of sequencing methodologies | |
| Analysis tools | clustering and fold change analysis emerging as standard tools, but tools only partly integrated with databases | standard search tools such as Blast (Altschul et al. 1990) fully integrated with databases |
[i] Comparison with sequence analysis/structural genomics regarding integration of databases, data standards, and computer analysis tools.
[ii] National Center for Biotechnology Information (1999);European Bioinformatics Institute (1999).