Schizosaccharomyces genus

Ascomycete fungi also known as the fission yeasts. Contains the widely used model organism Schizosaccharomyces pombe and the recently sequenced Schizosaccharomyces japonicus. Fission yeast was isolated in 1893 by Lindner from East African millet beer and the S. pombe species name is derived from the Swahili word for beer (Pombe).

For more information see the Broad Institute Fungal Genome Initiative (S. japonicus) or Wellcome Sanger Institute (S. pombe).

Tandem Repeats and their identification

Tandem repeats are contiguous approximate copies of repeated DNA sequences constructed in a head-to-tail arrangement. Identified here in both S. pombe and S. japonicus using Gary Benson's Tandem Repeat Finder program (links). Protein coding (CDS) and non-coding regions (Non-CDS) were considered seperately and TRF was run using alignment parameters of 257 (+2 for a match, -5 for indels and -7 for a mismatch) and a minimum alignment score of 32 for both protein coding and non-coding regions in S. japonicus and in S. pombe 42 and 51 respectively. Ouptut from TRF is given in the tables here along with an additional search for tandem repeat orthologs in S. pombe and S.japonicus protein coding regions.

Schizosaccharomyces Tandem Repeat Database

Schizosaccharomyces TRDB is a relational tandem repeat database that relates tandem repeats to their corresponding genomic regions and to orthologs in S.pombe or S. japonicus. It stores both perfect and imperfect repeats.


There are 3 main types of search for user queries:

  • 1. Basic species search

    Individual searches for the S. japonicus and S. pombe individual databases. Allows user to search by chromosome (or supercontig), region, tandem repeat length, repeat unit length, copy number, feature (CDS or Non-CDS) and consensus. Consensus search allows user to input a consensus sequence and supplies options to search for a:

    • - consensus identical to input
    • - consensus containing the exact user input (with circular permutation searching)
    • - consensus matching complement of user input

  • 2. Advanced search

    Allows user to choose to search either each database individually or both together. Contains search options from basic searches and has the additional search options for period size, percent matches, tandem repeat ID and gene names.

  • 3. Ortholog search

    TRF output on results page contains a check box at the end of each record. If one or more boxes are checked by the user a search is made of the coding region ortholog database and allows user to view any orthologs. Selecting tandem repeat reverts back to the full TRF output for that individual repeat. Ortholog matches are ordered by percentage similarity, highest first.

N.B. Due to the length of some consensus sequences, to view full consensus please click consensus and look at the bottom of the page to see the full sequence.

For any questions please see links page for contact details.