PombeWeb: People and events
- Fission yeast lab home pages and faculty listings
- online lists, including email addresses, where to find the Yeast Newsgroup, and information
about the pombelist email list
- Where to get pombe strains, libraries and plasmids.
- Fission yeast meetings
- Other sites with a wide range of information
- Genome sequencing, analysis, and searches . Most of these links have been moved to the
genome and sequence analysis page
- Federally funded (US) grants that use pombe
- NIH S. pombe model organism page
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!
- 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
- 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 http://listserver.ebi.ac.uk/mailman/listinfo/pombelistt">Pombelist info at the EBI. Send posts to firstname.lastname@example.org.
- NIH now has an Trans-NIH S. pombe page as part of their list of Model organisms for Biomedical Research
- General information about lots of pombe genes from the PUMA project (Phylogeny of the Unicellular Organisms Metabolic Pathways Alignments)
- Information about pombe HREF="http://megasun.bch.umontreal.ca/People/lang/species/spo/spombe.html"> mitochondria
- Nurse lab manual on Biowiki; . This was original written by a group of students and postdocs (including Susan) in Paul Nurse's lab in the early 90s and has been updated since.
- An answer to that thorny question Just how distant IS pombe from cerevisiae?
- There's a list of pombe links from NIH
- Atsushi Isoai's yeast links page has diverse links covering all yeasts
- Toru Nakamura's home page has links related to pombe, telomeres, and replication
- Fission yeast has gone commercial! Check out this page for some information on commercially available expression systems.
- A list of useful yeast sites from Nature Reviews Genetics (ditto)
- Sequence analysis bookmarks, including links to organism genome sites, blast servers, etc.
Curated Budding Yeast OrthologuesA 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/
Searching curated orthologues in GeneDBYou 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.
Eukaryotic Orthologues and associated Gene Ontology (GO) AnnotationYOGY 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
Genes with no apparent orthologuesIf 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)