SGD Help: Reference Sequence

The annotation of the Saccharomyces cerevisiae strain S288C Reference Sequence in SGD is described on Chromosome Summary and Chromosome History pages. The Chromosome Summary provides Basic Information and access to Resources. The Chromosome History displays the sequence and annotation history of a particular chromosome in SGD. This includes information about new genes or features, updates to the sequence and/or annotation, and other related notes.

Please note: As of June 19, 2006, the Chromosome History replaces the "Table of Sequence Updates," the "Table of Sequence Annotation Changes," and all associated pages.

Contents

  1. Chromosome Summary
    1. Basic Information
    2. Resources
  2. Chromosome History
    1. Sequence Changes
    2. Annotation Changes

Chromosome Summary

The SGD Chromosome page is divided into two sections, BASIC INFORMATION and RESOURCES.

Basic Information

The Basic Information section lists general information regarding a particular chromosome, including the following:

  • Feature Type: The Feature Type for all chromosomes is simply "chromosome".
  • Sequence Information: The Sequence Information field lists the chromosomal number and full coordinates, as well as links to two map displays (ORF Map and GBrowse). Also listed are the dates on which the sequence and annotation of that chromosome were last updated. The phrase "Most recent" is hyperlinked to the Chromosome History for that particular chromosome. A list of all loci contained within a chromosome may also be retrieved via a preloaded query to SGD's YeastMine.

Resources

The Resources section provides resources for additional analysis and information retrieval for a particular chromosome.

  • Literature: Searches PubMed for papers that mention a particular chromosome as well as Saccharomyces cerevisiae.
  • Retrieve Sequences: Links to Chromosomal sequence retrieval and Gene/Sequence Resources tools.
  • Sequence Analysis Tools: Links to Restriction MapperBLAST, and Primer Design tools.
  • Maps and Displays: Links to the Chromosomal Features Map.

Chromosome History

A table lists the number and dates of sequence and annotation changes to each chromosome. Each chromosome number is linked to the Chromosome History page for that chromosome.

At the top of each Chromosome History page are listed the numbers of sequence and annotation changes that have been made to the chromosome's systematic reference sequence since its intial release on 1996-07-31, as well as the number of chromosomal features that have been affected by these changes. Note that some changes may have affected more than one overlapping or adjacent feature, or some features may have been updated more than once, so that the number of changes may differ from the number of affected features. Also included is a link to the directory on SGD's Downloads site that contains current and archived versions of the chromosome's sequence and annotation records.

The Chromosome History contains the following two sections:

Sequence Changes, including any resulting annotation changes

This section displays SGD curator notes describing sequence changes that have been made to the chromosome's systematic reference sequence, as well as any annotation changes that resulted from those sequence changes.

Included above each note is a data row(s) containing information in the following columns:

  • Date: the date the change was made
  • Affected Features: names of the features affected by the change, hyperlinked to their respective Locus Summaries
  • Start Coordinate of Change: the coordinate of the first nucleotide involved in the sequence change
  • End Coordinate of Change: the coordinate of the last nucleotide involved in the sequence change
  • Type of Change: the type of sequence change (deletion, insertion, or substitution)
  • Old Sequence: the previous version of the sequence (pre-change)
  • New Sequence: the updated version of the sequence (post-change)

The default sorting of the Sequence Change table is by Date with the most recent change at the top of the list. The column headings for Affected Features, Start Coordinate of Change, and Type of Change are clickable for ascending or descending sorting on those columns. The first click on each of these column headers will produce ascending sorting on that column, the second click will produce descending sorting, and subsequent clicks will alternate between the two.

Annotation Changes without sequence changes

This section displays SGD curator notes describing annotation changes that have been made to the chromosome, that specifically did NOT result from sequence changes. These types of changes can include the addition of a new feature, deletion of a feature, merge of one feature into another, a change in the annotated position of a start or stop codon, etc.

Included above each note is a data row(s) containing information in the following columns:

  • Date: the date the change was made
  • Affected Features: names of the features affected by the change, hyperlinked to their respective Locus Summaries

The default sorting of the Annotation Change table is by Date with the most recent change at the top of the list. The column heading for Affected Features is clickable for ascending or descending sorting on that column. The first click on this column header will produce ascending sorting, the second click will produce descending sorting, and subsequent clicks will alternate between the two.

Go to Chromosome Summary | Chromosome History