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T. thermophila Genome Resources
at the Following Sites
The Institute for Genomic Research (TIGR)
General information about the T. thermophila Macronuclear Genome
Sequencing Project.
T. thermophila FTP server - Download files containing TIGR's genome
sequence assemblies, preliminary gene predictions, and more.
T. thermophila Gene Index - Information about genes and EST sequences of
T. thermophila.
T. thermophila BLAST
server - Search the macronuclear genome assemblies and preliminary gene predictions.
TIGR'sT. thermophila Genome Annotation Database - Search for preliminary gene annotations through TIGR's MANATEE annotation system.
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:
- GFF3 files containing the information provided by TGD via GBrowse,
a GMOD tool;
- 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.
- 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.
- 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);
- 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,
- 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
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