SGD Help: SGD Worm-Yeast Protein Comparison
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The Worm-Yeast Protein Comparison page allows the user to enter
- a yeast gene or ORF name,
- a worm gene or ORF name, or
- 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).
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.
- 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).
|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")
||Some ORFs have a "-A" or "-B" at the end (e.g. YDL130W-A,
|Worm gene name
||3 letters + "-" + a number
|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
||Text using one or more words or parts of words (search will treat
your entry as a wildcard entry)
||sec, secretion, dehydrogenase, MAP kinase
- 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:
||Keyword search result: Similarity groups containing "sec" in their
||Gene/ORF name search result: List of gene/ORF names which contain
- When using a wildcard character(*), you must include at least 3
characters in addition to the wildcard.
- The search is not upper/lower case sensitive.
More Specific Guidelines for Searching:
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.
- 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
- 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.
- 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).
- SGD Pages
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Description and Methods