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Simple Search

Simple search provides access to so called canned queries, which can be parameterised by the user. The queries have been organised into the following groups according to the scope of the analysis and the type of data queried.


Groups of queries:

  • Annotation of proteins in clusters

    Collection of queries to retrieve all available annotation for proteins in particular MCL or OrthoMCL clusters. Annotation includes protein sub-cellular localisation predicted using PSort and Wolf-PSort, prediction of secretory proteins using SignalP, Pfam motifs identified for each protein, Gene Ontology annotation and KEGG pathways the proteins are involved in. Clusters can be specified either by their identifier or in terms of their contents, such as a particular protein or proteins with a particular annotation, such as a specific sub-cellular localisation.

  • Cellular localisation analysis

    Queries in this category can be used to retrieve the sub-cellular localisation for a particular protein, or retrieve proteins with the same sub-cellular localisation as a given protein. Furthermore, all proteins with a given localisation can be retrieved. Localisations have been predicted using PSort and Wolf-PSort.

  • Essential yeast genes cluster analysis

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

  • Essential yeast genes orthology analysis

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

  • 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).

  • Functional annotation analysis

    Queries to retrieve Gene Ontology annotation or Pfam motifs for a given protein. Furthermore, all proteins with a particular GO annotation or Pfam motif can be retrieved.

  • Genomic analysis

    Collection of queries for general genomic analyses.

  • 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

    Queries in this group provide a general analysis of the OrthoMCL 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.

  • Pathway analysis

    Queries to retrieve Enzyme annotation for a given protein or the pathways it is involved in. Furthermore, all proteins with a particular Enzyme annotation or those involved in a particular pathway can be retrieved.

  • Redundancy analysis

    The queries in this group analyse MCL and OrthoMCL clusters containing proteins of a given genome in terms of the number of proteins of that given genome present.

  • Secretome analysis

    Queries in this category can be used to retrieve the SignalP prediction, i.e., whether it's been predicted to be secretory or non-secretory. Furthermore, all secretory or non-secretory proteins for a given genome can be retrieved.

  • Transcript abundance

    Collection of queries for transcript abundance analyses. These queries are able help in identification of genes that may be highly expressed in a particular growth conditions. Information of these genes and conditions can also be retrieved.


e-Fungi has been funded by the BBSRC Bioinformatics and E-science Programme II