TGD Resources

J. Craig Venter Institute (JCVI: formerly TIGR, The Institute for Genomic Research)

  • T. thermophila FTP server - Download files containing TIGR's genome sequence assemblies, preliminary gene predictions, and more. The most recent files are found in the Final Assembly 2008 folder.
  • DFCI T. thermophila Gene Index - Information about genes and EST sequences of T. thermophila.
  • JCVI T. thermophila BLAST server - Search the v.2004 - v.2006 macronuclear genome assemblies and preliminary gene predictions.

    National Center for Biotechnology Information (NCBI)

  • T. thermophila Whole Genome Shotgun (WGS) Sequencing Project
    A summary of miscellaneous genome information is provided, as well as links to the RefSeq accession number NZ_AAGF00000000, the GenBank accession number AAGF00000000, the RefSeq and GenBank FTP sites, the Genome Project Overview, the Contigs, and NCBI's BLAST server.

  • T. thermophila Macronuclear Genome Sequence
    The macronuclear genome was sequenced by Eisen et al. 2006 and submitted to GenBank under the accession number AAGF00000000

  • T. thermophila Genbank Sequences
    A list of previously sequenced genes, cDNAs, and genomic regions, including the complete sequence of the T. thermophila mitochondrial genome.

    TGD

  • BLAST
    Use WU BLAST 2.0 to search sequences from Tetrahymena and related organisms that are present in international sequence databases (GenBank, EMBL, DDBJ, RefSeq, SwissProt, PIR, PRF, and PDB), including the macronuclear genome sequence determined by TIGR. The protein and DNA sequence datasets searchable at TGD are available via FTP.

  • GBrowse
    Browse the T. thermophila genome sequence for genes, keywords, and short nucleotide sequences using this genome browser, available from the Generic Model Organism Database (GMOD) construction set.

  • Tetrahymena FTP server
    In the genomic feature directory you can find the following files to download:
    1. GFF3 files containing the information provided by TGD via GBrowse, a GMOD tool;
    2. a file named Tt_IPRScan1.lst that summarizes protein domain information determined by using the InterProScan tool to query each T. thermophila gene model against the InterPro database.
    3. a file named Tt_besthits.lst that contains the results of NCBI BLASTP analysis using each T. thermophila protein sequence to query predicted protein sequences from several model organisms.
    4. a mapping file named Tt_ID_Mapping_File.txt that lists all of the identifiers that have been used for the T. thermophila gene models (eg. TTHERM_IDs, Manatee IDs, PreTt IDs, and TGDIDs);
    5. a mapping file named GeneName_Alias.txt that lists the standard and non-standard names for the T. thermophila genes when multiple names have been published for a given gene; and,
    6. a file named GeneName_Ttherm_Annot.txt that lists all of the T. thermophila genes that have been experimentally studied, a manually annotated description of the genes, and a mapping of these genes to the corresponding gene model.
    In the sequence directory, under the subdirectory, public sources, you can find the protein and DNA sequence datasets that are searchable at TGD via BLAST.

  • TGD's T. thermophila Gene Index
    An index of T. thermophila genes that have been given Standard Gene Names by members of the research community.

  • Mapping file of identifiers used for the T. thermophila gene models
    This mapping file includes TTHERM IDs, Manatee IDs, PreTt IDs, and TGDIDs.

    Other Tetrahymena Resources

  • Tetrahymena EST sequences at the Taxonomically Broad EST Database (TBestDB)
    Sequence data from a variety of Tetrahymena EST libraries can be accessed from TBestDB,a repository for EST data from a wide range of eukaryotes. Most of the data contained in TBestDB has been generated by the Protist EST Program, a collaboration of labs across Canada.

  • Tetrahymena Genetic Mapping Data