Table 2 Canned query groups currently provided

Annotation of proteins in clusters

Queries in this group retrieve annotation of all the proteins in particular clusters. The annotation consists of PSort, Wolf-PSort and SignalP predictions, as well as GO annotations, Pfam domains, Enzyme annotation and pathways for each protein, as well as its assignment to a particular MCL and OrthoMCL cluster. The clusters can either be chosen by providing an identifier of a particular cluster or they can be based on the proteins they contain, such as proteins with a particular GO annotation or a particular cellular localisation as predicted by PSort or Wolf- PSort.

Cellular localisation analysis

This group of queries retrieves the cellular localisation for proteins as predicted by PSort and Wolf-PSort. It also retrieves proteins with a particular predicted cellular localisation.

EST analysis

Collection of general EST analyses. Information available include group/hierarchy structure of ESTs and genes as well as number of homologs of genes in all genomes in the database.

Essential yeast genes cluster analysis

Queries to retrieve Mcl Clusters containing proteins of a given genome and proteins of essential or non-essential yeast genes.

Essential yeast genes orthology analysis

This group of queries analyses clusters containing a given genome and proteins of essential or non-essential yeast genes in terms of the number of genomes present in those clusters.

Functional annotation analysis

Queries in this group enable the retrieval of Gene Ontology or Pfam annotation for a given protein, or the retrieval of proteins with a given annotation.

Genomics analysis

Collection of queries for general genomic analyses, such as retrieving the exons of a particular gene.

MCL cluster analysis

Queries in this group provide a general analysis of the MCL clusters in the database. Clusters containing proteins of a given genome, or a group of genomes, such as plant pathogens or filamentous fungi, can be retrieved. Furthermore, clusters that contain more or less than a given percentage of proteins of a given genome can also be obtained.

OrthoMCL cluster analysis

This group of queries provide a general analysis of the OrthoMCL clusters in the database. The queries in this group are similar in scope to the queries in the MCL cluster analysis group.

Pathway analysis

Queries provided in this group retrieve pathways and enzyme annotations for a particular protein as well as all the proteins in a given pathway or with a particular enzyme annotation.

Redundancy analysis

The query in this group analyses the redundancy in a given species. Genome redundancy is determined by counting the number of proteins of that given genome in MCL clusters.

Secretome analysis

To retrieve the SignalP prediction for a given protein or proteins with a given SignalP prediction, i.e., secretory or non-secretory proteins, queries in this group can be used.

Transcript abundance

Collection of queries for transcript abundance analyses. These queries enable the identification of genes that may be highly expressed under a particular growth condition. Information of these genes and conditions can also be retrieved.