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CGD Batch Download Tool

Help

This resource allows simultaneous retrieval of DNA and Protein sequences for a list of Standard gene names or Feature names. Data that can be retrieved using this tool is included in one or more files on our download site. If you are interested in retrieving data for a large number of features, please visit the download site.

Gene/Feature names can be entered in one of three ways:
1. direct entry
2. upload from a file
3. chromosomal coordinates (enters all features/gene names between these coordinates)

Note: Please do not use Alias Gene names in your input list.




Step 1: Your Input
Option 1. Enter Feature/Standard Gene names (separate by return:)


    OR

Upload a file of Feature/Standard Gene names


Examples:
Gene - ACT1
ORF - orf19.2203
CGDID - CAL0001571

AND

Select an Assembly:
Option 2. Pick a root sequence name

Then enter coordinates (optional):
to

If no coordinates are entered all the features in the selected chromosome will be retrieved.

OR

Upload a file of chromosomal regions (coordinates are optional) with the following tab-separated columns:
chr start_coordinate stop_coordinate
For example:
Ca21chr3 1356 20455
Ca21chr4 11331 18001
Ca21chr6 9856 100010
Step 2: Choose the type of data that you want to retrieve (You can select multiple types)
Please check the help page for details on the output file format.
  • Sequence data
    • Genomic DNA (DNA sequence with introns)
    Genomic DNA + 1 kb upstream and 1 kb downstream of flanking sequence
    Coding Sequence (DNA sequence without introns)
    ORF Translation (Protein Sequence)

  • Other data
    • Chromosomal Feature information including gene names, coordinates, description and CGDID (in CGD_Feature.tab file format)
    Gene Ontology (GO) Annotations (in gene_association file format)
    Phenotype
    S. cerevisiae Ortholog or Best hit
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    CGD Copyright © 2004-2008 The Board of Trustees, Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.