BLAST/BLAT Help
TGD offers two types of sequence similarity searches at our website:
the Washington University Basic Local Alignment Search Tool (WU BLAST 2.0)
and the BLAST-Like Alignment Tool (BLAT). There are multiple datasets
available for searching at TGD, each listed below and described in
more detail. All datasets exist in both nucleotide and
protein forms. For example, searching the "TIGR Gene Predictions"
dataset with BLASTN, TBLASTN, TBLASTX, BLAT, or TBLATN will automatically select the nucleotide version
of the "TIGR Gene Predictions" sequences when the search is
performed. Selecting BLASTP or BLASTX will automatically select the protein version
of the dataset. All datasets can be accessed via the TGD FTP server.
The following datasets are currently available for searching at TGD
T. thermophila (GenBank):
All T. thermophila (Taxonomy
ID #5911, as listed in the NCBI Taxonomy
Browser) sequences submitted to GenBank, excluding entries to
the Whole
Genome Shotgun (WGS) sequence repository (which contains the entire genome
sequence as determined by TIGR).
T. thermophila Macronuclear Genome (TIGR v2):
T. thermophila macronuclear genomic scaffold sequences determined by TIGR. Each of
these sequences has been deposited in the Whole
Genome Shotgun (WGS) sequence repository at GenBank. Searching this
dataset will return links to the
GenBank records for the
scaffolds that align with the query sequence. A link to TGD GBrowse
is also provided for each aligned region, allowing easy access to the relevant
region of the genome. See GBrowse
Help for assistance using this tool to browse and access sections
of the macronuclear genome sequence.
TIGR Gene Predictions:
Coding regions of the macronuclear genome and their protein translations, predicted by TIGR on
5/4/04.
Oligohymenophorea (GenBank):
All sequences from ciliates belonging to Family Oligohymenophorea (Taxonomy
ID #6020, as listed in the NCBI Taxonomy
Browser) submitted to GenBank, excluding entries to the Whole
Genome Shotgun (WGS) sequence repository (which contains the entire genome
sequence as determined by TIGR).
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