PombeNet
Goin' fission....

PombeWeb: People and events

Stacks Image 127

People working with pombe

This list includes full-time pombe labs as well as those who have partial pombe efforts--over 80 groups world wide. However, many pombe groups are not on the web, so this list is not a complete roster of the pombe community. We are particularly missing many of our colleagues in Japan. If you know of additional URLs , or have corrections, please send them to us and we will add them. We will also remember former pombe folk who for one reason or another have moved out of academic science. We particularly thank Richard Egel who in spring 2008 reviewed and updated these links.

For colleagues working in S. cerevisiae, go to the SGD database. The SGD database is not limited to budding yeast--add your own name and contact info, and participate the global yeast community!

Need strains or plasmids?


  • The National Collection of Yeast Cultures in Norwich, England has an excellent and wide-ranging pombe collection.
  • The AddGene database is another repository many labs are using
  • The FYSSION project at Sussex is building genomics and genetics tools , starting with strains and mutants. Investigators can apply to screen a large collection of novel TS mutants for phenotypes of interest.
  • The Yeast Genetic Resource Center Japan. This includes strains, plasmids and libraries. Resources are available at no (or low) charge to academic labs. You are encouraged to deposit additional reagents for public distribution.
  • In the US the ATCC has developed a small collection of pombe strains and plasmids to get you started. This is a good source for vectors and wild type strains. Check out the ATCC pombe page. See the vector page for information on the Hiraoka lab GFP fusion library
Stacks Image 128

Online lists


  • The Bionet newsgroup Yeast is a good place to ask questions and keep up on what's happening in the community. Postdoc positions are also posted there. (Also see the postdoc listings on our community page) The term yeast is inclusive; the group includes S. cerevisiae and S. pombe as well as occasional forays into Pichia, Candida, and others.
  • The pombelist mailing list runs from the Sanger Institute. "This mailing list is primarily to inform subscribers of developments and progress of data and tools, relating to the S. pombe Genome Sequencing project. It will include periodic sequencing total updates, sequencing reports, details of new new releases and features of the S pombe database POMBASE, and any other information which might be useful to the pombe community."
  • To subscribe to the list go to Pombelist info at the sanger center.
Stacks Image 129

Meetings


Stacks Image 130

Other sites

Stacks Image 131

Search for US federally funded grants that use pombe:

Stacks Image 132

Curated Budding Yeast Orthologues

A manually curated list of S. pombe/S. cerevisiae orthologs covering 75% of fission yeast gene products is available. Alignments used to make orthology inferences are submitted to the Pfam protein family database. You can subscribe to the mailing list 'Yeast_orthologous_groups' to receive the curated ortholog inventory and updates as a spreadsheet. http://lists.sanger.ac.uk/mailman/listinfo/yeast_orthologous_groups/
Stacks Image 133

Searching curated orthologues in GeneDB

You can search for curated orthologs of individual S. cerevisiae genes in GeneDB http://www.genedb.org/genedb/pombe/. You must use the S. cerevisiae systematic identifier (e.g YOR073W) and the "Full Content Search" box.
Stacks Image 134

Eukaryotic Orthologues and associated Gene Ontology (GO) Annotation

YOGY is a tool which uses the major orthology predictors (KOGS, OrthoMcl, Inparanoid, Homologene) to identify potential orthologs in the major model eukaryotes and allows the user to retrieve GO terms manually associated with these orthologs by curators at the Model Organism Databases. YOGY is accessible from
http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ OR via a link from
the "Database Cross-References" section of every GeneDB_Spombe gene page
Stacks Image 135

Genes with no apparent orthologues

If you are working on one of the 474 gene products which have no homologs identified (357 sequence orphans, 71 published genes with no apparent homologs, 46 S. pombe specific families), the Japonicus genome at the Broad Institute may provide new insights:

It is possible that a PSI Blast search (Position-Specific Iterated BLAST) with the japonicus ortholog as a query will provide a good enough seed alignment to detect more distant orthologs which were missed by searching with the fission yeast sequence. (Note that current 'non conserved' status assignments in GeneDB have not been systematically checked against Japonicus)
Stacks Image 136

TREEFAM

http://www.treefam.org/Treefam is a database of phylogenetic trees and also an ortholog database. Because Treefam infers orthology using trees it can be more accurate than some of the 'Blast based' orthology prediction methods. Although developed for animal genes it tries to include S. cerevisiae and S. pombe as outgroups. With Treefam distant relationships are sometimes missed, however, the incidence of false positives is low. Treefam will become increasingly useful to assess how pombe genes are related to animal families as further families are curated.
Stacks Image 137