Biology Reference
In-Depth Information
2. Annotation Pipeline of the Dictyostelium
discoideum Proteome in Uniprotkb
2.1. Creating a Complete Proteome Set Across
Swiss-Prot and TrEMBL
Not all organisms whose genome has been sequenced are included in the
complete proteome sets of UniProtKB. We consider as a “complete pro-
teome” those sets of proteins that originate from genomes which have
been fully sequenced and for which good-quality gene prediction mod-
els are available. These criteria are fulfilled for
Dictyostelium discoideum
and for an increasing number of other eukaryotic organisms such as
Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana
, and
Saccharomyces cerevisiae
, as well as for a plethora of bacterial and archaeal
species. The up-to-date list of available complete proteomes can be retrieved
at http://www.uniprot.org/taxonomy/?query=complete%3ayes/.
Defining and deciding which proteins belong to a complete pro-
teome set is often not a trivial task. Prior to our annotation jamboree,
TrEMBL contained three types of protein entries for
D. discoideum
:
(1)
entries derived from the predicted gene models of the submitted
genomic sequence;
(2)
entries derived from the predicted gene models of a preliminary
sequence of chromosome 2, as carried out by one member of the
genome sequencing consortium in 2002
6
; and
(3)
entries derived from full-length cDNAs or from genomic DNA seg-
ments which have been submitted over the last 20 years by individual
Dictyostelium
laboratories.
To add a bit of complexity to this situation, not all proteins were linked to
the same taxonomic node. The proteins from the genome sequence were
stored as originating from the taxonomic identifier (TaxID) 352 472,
which corresponds to
Dictyostelium discoideum
strain AX4 (the specific
strain selected to be sequenced by the genome consortium); while the two
other categories of entries were said to originate from TaxID 44 689,
which corresponds to the generic
Dictyostelium discoideum
. In agreement
