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SGD Help: SGD Worm-Yeast Protein Comparison


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Description

The Worm-Yeast Protein Comparison page allows the user to enter either:

  1. a yeast gene or ORF name,
  2. a worm gene or ORF name, or
  3. a keyword(s)

and retrieve results relevant to the entry based on the comparison of the entire complement of predicted proteins from C. elegans and S. cerevisiae (this analysis is described in detail in Chervitz et al., (1998).  Science 282:2022-2028).

Using the SGD Worm-Yeast Protein Comparison

Summary Guidelines for searching:

Note: All search terms are first checked against the lists of worm and yeast gene/ORF names by the search program. If an exact match is not found, the term is then searched against the Similarity Group Descriptions as a keyword. Thus, exact matches for gene/ORF names must be entered in order to obtain the results for the desired gene OR a wildcard character (*) must be used in the search.

  1. In the absence of a wildcard character (*), a gene or ORF name must be provided in the correct format (see table below) and with the exact name in order to be recognized (this includes hyphens, periods).

    Entry Format Examples Exceptions
    Yeast gene name 3 letters followed by a number ACT1, CDC28, HOD1 Ribosomal protein nomenclature
    e.g. RPLA1, RPLA2
    Yeast ORF Name "Y" + chromosome letter ("A" - "P") + centromere side ("L" or "R") + 3-digit number + strandedness ("C" or "W") YFL039C, YAL066W Some ORFs have a "-A" or "-B" at the end (e.g. YDL130W-A, YDR034W-B)
    Worm gene name 3 letters + "-" + a number let-60, GST-1
    -
    Worm ORF Name These correspond to the clone names from the sequencing project and have no standard pattern R03D7.6, ZK546.11, Y32G9A_367.c
    -
    Keyword(s) Text using one or more words or parts of words (search will treat your entry as a wildcard entry) sec, secretion, dehydrogenase, MAP kinase
    -

  2. Any term without a wildcard appended which is not found on the gene/ORF lists will be viewed as a keyword by the search program. If this term is not found to match any similarity group descriptions, a wildcard character (*) will automatically be added to it and the search rerun against the a list of all worm and yeast gene and ORF names. Thus, the wildcard should not be added by the user entering a keyword(s). The example below shows the difference between using vs. not using a wildcard character:

    Entry Result
    sec Keyword search result: Similarity groups containing "sec" in their description
    sec* Gene/ORF name search result: List of gene/ORF names which contain "sec"

  3. When using a wildcard character(*), you must include at least 3 characters in addition to the wildcard.

  4. The search is not upper/lower case sensitive.

More Specific Guidelines for Searching:

  1. Entering a complete worm or yeast gene/ORF name: You can enter either a yeast gene name, yeast ORF name, worm gene name, or worm ORF name according to the guidelines provided in the table found in the above section. In the absence of a wildcard character (*), all names must be provided in their exact format (upper/lower case excluded).

  2. Using the wildcard character (*) to enter a partial worm or yeast gene/ORF name: You can use the wildcard character (*) behind 3 or more characters (you must provide at least three characters) to search for all potential matches to the entered text. This will bring up an intermediate results page which will provide a list of gene/ORF names in which your entry is found. For instance, a search for "sec*" brings up a list of 41 different yeast SEC genes.

  3. Entering a keyword: Enter one or more words or partial words for a keyword search. All keyword searches should be performed without using the wildcard character (*). Using the wildcard character results only in matches to gene/ORF names (if there are any) rather than keywords (see example in the above table).

Accessing the SGD Worm-Yeast Protein Comparison

This page is considered the Worm-Yeast Home page, and can be accessed from the menu top on all pages showing the worm-yeast logo.

Other Relevant Links

  1. SGD Pages
    1. Shared & Unshared Similarity Group Summaries
    2. Download Worm-Yeast Datasets
    3. Worm-Yeast BLAST Summaries
    4. General Description and Methods

Associated Glossary Terms


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