Tetrahymena Genome Database

Quick Search: Genome Resources Genome Browser BLAST & BLAT Textpresso (Full-Text Search) Tetrahymena Literature Tetrahymena Biology Community Information Stock Center at Cornell Tutorial Help About TGD Home	TGD Help: Quick Search Help Overview TGD's Quick Search, located in the upper left hand corner or in the toolbar at the top of the page, can be used to query for information within the Tetrahymena Genome Database (TGD). The following categories are searchable by keywords: gene names and aliases; gene descriptions; Gene Ontology (GO) terms and synonyms; predicted protein domains; homologs; paper abstracts; colleagues; and authors of references stored in TGD, PubMed IDs, and GO IDs. Wild Card Searches (*) Quick Search is case insensitive and supports wildcard characters, which may be used to broaden your search. You may use wildcard character(s) in the beginning and/or end of a search term to indicate the location(s) where any text will be tolerated. If you are unsure of a complete gene name, for example, you may query "pdd*" to return all of the pdd genes, PDD1, PDD2 and PDD3. If you query "pdd" no matches to gene names will be found because there is no gene named exactly PDD; if you query "pdd1" one gene name match will be found since there is a gene PDD1 in TGD. If you are unsure of a colleagues name or its spelling, for example, you may query "Johns" to return all colleagues whose last name begins with those letters, such as Johnson and Johnston. If you are interested in finding Tetrahymena genes that are or are predicted to be serine threonine kinases, you can query "ser* kinase" and get matches in the categories of gene descriptions, GO terms, domains, homologs, and paper abstracts. Since many of our annotations to the predicted gene models are electronic and use protein names and descriptions from different databases, different terminologies may be used to describe the same thing in TGD. By querying with a broad term, such as "ser* kinase" you are able to find matches to a variety of similar terms, such as serine threonine kinase, ser/thr kinase, serine/threonine kinase, serine/threonine protein kinase, and serine-threonine kinase to name a few. If you wish to retrieve information on phosphorylases, phosphatases, and 3'- and 5'-phosphatases, you may query "*phosph*", which uses two wildcard characters, one in the beginning of the search term and one in the end. Note: The wildcard character may NOT be used to broaden a purely numerical query for a PubMed ID or a Gene Ontology ID. Search Results The results for your Quick Search can include matches in one or more of the following categories: Gene name (standard gene name, preliminary gene name provided by TIGR and TGD, or aliases) Gene Description Gene Ontology (GO) term (a GO term name or synonym) Domain Homolog Paper Abstract Colleague Author of a reference stored in TGD PubMed ID GO ID If your query matches keywords in more than one search category, then you will be redirected to the summary TGD Quick Search Results page that lists the number of matches to each of the categories. This will enable you to view all of the information in TGD that may be relevant to your query. You can click on the individual categories to view all of the results that matched your search criterion within that category. If your query only matches one gene name and nothing else in any of the other categories, then you will be redirected to the gene page. If your query matches only information in one of the categories, you will be redirected to the specific results page for that category. The search results page for the individual categories are described below. Gene Names If your query matches more than one gene then the search results will be displayed in a table with your search criterion highlighted in yellow. The table will contain the following columns: the result that matches your search term; the gene name; the sequence ID; any aliases associated with the gene; and, the description for the gene. The match name is a hyperlink to the locus page for that gene. Gene Descriptions If your query matches one or more words in a gene description, a concise summary of the gene/gene product in TGD, then the results will be displayed in a table with the following columns: a description of the gene/gene product with your search criterion highlighted in yellow; and, any genes associated with the description. The gene name (which may be displayed as a standard gene name, a TIGR or TGD preliminary gene name, or a TGD identifier) is a hyperlink to the gene locus page. The gene descriptions searched include manually curated summaries that are written for published genes, and computationally derived summaries obtained from TIGR for the preliminary gene models. Gene Ontology Terms If your query matches one or more GO terms, then the GO term results will be displayed in a table with the following columns: the GO term with your search criterion highlighted in yellow; the GO synonym; the GO aspect (for example, molecular function, biological process or cellular component); and, any genes associated with the GO term. The associated gene name (which may be displayed as a standard gene name, a TIGR or TGD preliminary gene name or as a TGD identifier) is a hyperlink to the gene locus page. Domains If your query matches one or more predicted domains, then the results will be displayed in a table with the following columns: the domain identifier; a description of the domain with your search criterion highlighted in yellow; and, any genes associated with the domain. The associated gene name (which may be displayed as a standard gene name, a TIGR or TGD preliminary gene name, or a TGD identifier) is a hyperlink to the gene locus page. The domain information is displayed on the locus page beside the subject header Domain Information, underneath the Provisional Annotation for TIGR's preliminary gene model. Homologs If your query matches one or more terms in a description of a homolog in TGD, then the results will be displayed in a table with the following columns: the homolog identifier; a description of the homolog with your search criterion highlighted in yellow; any genes associated with the homolog; and, the E-value for the BLASTp hit. The associated gene name (which may be displayed as a standard gene name, a TIGR or TGD preliminary gene name, or a TGD identifier) is a hyperlink to the gene locus page. Paper Abstracts If your query matches one or more words in a paper abstract in TGD, then the results page will list the citations for all of these papers, and provide hyperlinks to the reference, and if available, its abstract in TGD and PubMed. Colleagues The colleague search results page is titled TGD Colleague Search Result and displays a table that contains the following information: colleague name; the organization; and basic contact information such as phone number, fax number, and email address. The colleague name is a hyperlink to the full colleague information. Authors The author search results page is titled TGD Curated Papers, and displays a table containing the following information: the authors with your search criterion highlighted in yellow; and the complete reference citation, including links to the TGD curated paper page and the PubMed abstract. PubMed IDs PubMed IDs can be searched by the numeric portion only or the numeric portion with the prefix 'PMID:' or 'PubMed:'. If there is only one match and it is to a PubMed ID, you will be redirected to the TGD Curated Paper page for the reference with that PubMed ID. GO IDs GO IDs can be searched by the numeric portion only or the numeric portion with the prefix 'GO:'. If there is only one match and it is to a GO ID, you will be redirected to the GO Term page for that particular GO ID.
To contact TGD: Send email to ciliate-curator@genome.stanford.edu. Return to TGD Home