VchoCyc Release Note History

Version 7.6

Released on November 4, 2003

In this release, we have made putative functional assignments to 59 genes in VchoCyc. These functional assignments were made to fill pathway holes in the database. A pathway hole occurs when a reaction in a pathway does not have an assigned enzyme. The putative enzymes that fill these pathway holes were identified using a prediction program developed by Green and Karp (Green, 2003). Each enzymatic reaction linked to an enzyme by this program is identified by the evidence code "Computational Evidence: EV-COMP-HINF-FN-FROM-SEQ". The evidence code indicates the source of information as computationally-derived from sequence analysis with human review. The gene product field of the corresponding enzyme has also been updated to include the functional description of the reaction to which it has been linked. In total, 14 pathways were completed by filling these 59 pathway holes. A list of the remaining pathway holes may be found in the Missing Reactions Report.

Version 7.5

Released on August 28, 2003.

• 2610 predicted transcription units (operons) were added to VchoCyc. They were computed using the Pathway Tools operon finder (see Romero and Karp, Bioinformatics 2004). When a predicted transcription unit exists for a gene, it is displayed at the bottom of a gene page.

Version 6.0

Released on February 15, 2002.

• First release of VchoCyc.