ProDom CG1096 Statistics

Release date = December 2011

Sequence and Family Data

Proteins used to build ProDom CG1096: A subset of the proteins used to build ProDom 2010.1	3922998 (64.1 % of ProDom)
Number of complete genomes	1096
domain families with at least 2 sequences	618210 (+105% since CG267)
domain families	1839359 (+94% since CG267)
Families with a PDB link	27102
Families with a Prosite link (Patterns, Profiles)	99561
Families with a Pfam-A link	508081

How is Prodom-CG built ?

ProDom-CG (Complete Genome) is a version of the ProDom database which holds only data originating from the complete genome sequencing projects. This release was builded using the following process:

• Consider the complete genomes whose sequences are included inside Swissprot and Trembl (archeal,bacterial and eukaryotic genomes)
• Start from the corresponding Prodom version (usually newest version)
• Keep only the sequences belonging to one of those genomes
• Delete the ProDom families which are now empty
• Compute the multiple alignments and the consensus sequence for each remaining family
• Compute the links towards other databases and the statistical data

About the AC numbers

Because ProDom-CG is built from a release of ProDom, we can use an AC numbering scheme consistent with the corresponding ProDom release:

• The AC prefix is CG instead of PD
• When a ProDom family is conserved inside ProDom-CG, its AC number is kept unchanged
• When a ProDom family is deleted for Prodom-CG, its AC number is marked as invalid in ProDom-CG

This enabled us to provide users of the Graphics User Interface with two more buttons:

• From ProDom: access to the corresponding ProDom-CG family.
• From ProDom-CG: access to the corresponding ProDom family. The button may be absent, meaning the this family was empty in ProDom-CG

There are 23 archeal, 226 bacterial and 18 eukaryotic genomes in Prodom-CG.