The SPEED toolkit serves as an intuitive interface to the annotated resources housed within the SPEED database. These resources allow for the integration of evolutionary analyses into all aspects of biological research. For example, scientists working on a specific multi-genic disease may be able to use these tools to find potential targets for analysis at the bench or in clinical work.
Currently, the database houses information on over 17,000 human genes, with curated human-mouse ortholog records for over 15,500 gene pairs.
Please access the tools through the list of links below. Each tool is preceded by a brief (and hopefully helpful) description of its functions and operators. If you have any problems navigating the toolkit, find a broken link, or discover a tool that isn't working properly, please email the webmaster. |
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The gene search allows you to find ortholog sets within the SPEED database utilizing gene name,
gene keyword (e.g., histone or heme), or Reference Sequence ID number (from NCBI's Refseq database; e.g., NM_017231
for the PITP gene in rats). |
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GENE SEARCH:
browse all genes
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disease search allows you to find ortholog sets associated with specific human genetic diseases
as defined by the OMIM database (NCBI). Valid searches include disease name (e.g., diabetes, cancer) or OMIM ID number
(from NCBI's OMIM database; e.g., 147670, the identifier for the insulin receptor gene). |
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disease search:
browse all disease genes
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| The conserved protein domain search allows you to find specific functional regions (within proteins) identified by the PFAM consortium that are coded for by genes within the database. This search returns all ortholog sets within SPEED that contain an instance of your identified functional region/protein domain. For example, a keyword search on "heme" will return all ortholog sets that contain heme-binding domains (e.g., the progesterone receptor and hemopexin) and also heme-lyase domain-containing genes. Alternatively, a search by PFAM ID will yield narrower search results. |
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protein conserved domain search:
browse all protein domains
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The expression/histology/development search allows you to query the SPEED
database using tissue and expression terms from CGAP. Library information allows you to narrow the
search to look only for ESTs expressed in multiple libraries, which might enhance the reliability of these results. Please note that, unlike a differential display search, no attempt is made here to quantify the level of expression of each gene in the tissue. |
Expression/Histology/Development Search:
Data from Cancer Genome Anatomy Project (CGAP)
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| The metabolic pathways search allows the user to examine which ortholog pairs in SPEED exist in a specific metabolic pathway as defined by the KEGG website. Results from this search include all ortholog pairs contained in a specific pathway. |
Metabolic Pathways Search:
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The somewhat complicated motif search allows you to query proteins within SPEED to see if they contain specific user-defined amino acid sequences. These sequences conform to the rules for 'grep' regular expressions, and thus, brackets ('[' and ']') can be used to define a set of amino acids that are interchangeable at a given position in the sequence. A period ('.') is a wildcard, which means that any given amino acid can match at that position in the sequence.
For example, the search term RKK (arginine followed by two lysines) seeks an exact match and will only pull results where arginine is found followed by two lysines. On the other hand, the search term [RK]K seeks either an arginine or a lysine followed by a lysine. In a similarly "fuzzy" search, the search term R..K (R period period K) would match a sequence where arginine was followed by any two amino acids and then a lysine.
The boolean search term allows the user to define two different motifs that limit the search.
Finally, it is possible to exclude specific motifs from your set of returned results using the "excluded target information" fields. These fields function in the same way as those used for desired target motifs. For example, you may want to search a set of results using a specific domain, but produce results that exclude a known repeat domain.
The combined length of your target motifs may not exceed 30 sites (e.g., the search term "KKLYP" and the search term "[RTK][KL][LT]YP" are effectively the same length, as each one deals with the same number of sites in the motif). This is a hard limit, but does not include the length of excluded motifs.
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Motif Search:
If you have not used this search in the past please read this.
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