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SGD Help: Worm-Yeast Protein Comparison (Results Page)

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Contents


Description

The Worm-Yeast Protein Comparison results page is what is retrieved following submission of an entry off of the Worm-Yeast Home page. The entry on this page may be a worm or yeast gene or ORF name or a keyword. The results page is a summary of BLAST results and/or similarity group results for the specific gene/ORF entered. In the case of a keyword, it identifies all similarity groups having a Description in which the keyword is found. There are potentially three different types of results pages which may be obtained depending on the type of search performed. This Help document describes the types of pages which may be obtained and the information found on each.

Using the Worm-Yeast Protein Comparison (Results Page)

Types of Results Pages

  1. Results for gene/ORF name with an exact match: This type of page will appear if a gene/ORF name has been entered which is an exact match to a yeast or worm gene or ORF. It may contain one or more of the following:

    1. BLAST report: This is a direct link to the BLASTp report for the entered gene/ORF vs. the complete set of protein sequences from the other organism. For a further description of how this data was obtained, please see Description and Methods

    2. Presence in Shared Similarity Groups: This is a table of all shared groups (those containing worm and yeast members) in which the entered gene/ORF is found at various different P-values and alignments. There are 5 different columns in this table:

      1. P-value: P-value at which the similarity group occurs
      2. Alignment Constraint: this value will be either >80% or none, and indicates whether the alignment demanded >80% of the sequence be aligned
      3. Group Description: description given to the group based on pre-existing information about its members
      4. # Members: The total number of members (worm and yeast) in the group
      5. View type: Provides links to several different viewing options for the group (Rooted tree, Unrooted Tree, HTML alignment); These are described on the Displays page.

    3. Presence in Unshared Group(s): This is a table of of all unshared similarity groups (those containing two or more members, all from the same organism) in which the entered gene/ORF is found at various different P-values and alignments. Its organization is the same as that found for the Shared Similarity groups (see directly above).

  2. Results for wildcard (*) search for gene/ORF name with more than 1 match: This results page provides a list of all gene(s)/ORF(s) which match the wildcard entry. Clicking on a gene/ORF name in this list retrieves the comparison results page (described in section 1 above) for that gene/ORF.

  3. Results for a keyword(s) search: This type of results page lists groups which contain the keyword(s) in their Group Descriptons. There are two types of tables: one listing shared similarity groups, the other listing unshared similarity groups. Either one or both types of tables may be found on the keyword results page. The tables are of the same type as those described above.

Accessing the Worm-Yeast Protein Comparison (Results Page)

The Worm-Yeast Protein Comparison (Results Page) can be accessed by submitting an entry on the Worm-Yeast Home page.

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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