CGD Batch Download Tool

Help

This resource allows retrieval of sequence and other information for a list of chromosomal features (genes, or other annotated features such as centromeres). You may start with a list of feature names, or specify a chromosomal region(s) and retrieve information for the features within that region(s). If you wish to retrieve DNA sequences within particular coordinates, whether or not features are annotated within the coordinates, please use the Gene/Sequence Resources tool.

Get started with the Batch Download tool in one of two ways:
1. Enter a list of feature names or standard gene names (not aliases)
2. Specify a chromosomal or contig region to retrieve information about the features within that region
* Please note: Batch Download can only retrieve data for one strain at a time.

Each of these options allows you to enter the list directly or to upload it in a file.

Note: All of the information that can be retrieved using this tool is available in one or more files on our download site. If you need to retrieve data for a large number of features, please visit the download site.

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 strain:
AND
Select sequence: 		Option 2. Pick a chromosome/contig name:




Then enter coordinates (optional):
to

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

OR

Upload a file of chromosomal or contig regions:


Chromosome regions should be specified with the following tab or space separated columns (coordinates are optional) :

(i) chromosome/contig, (ii) start_coordinate, (iii) stop_coordinate

The file should contain regions from a single genomic assembly (19, 20, or 21).

C. albicans SC5314 Assembly 21 example:
Ca21chr3_C_albicans_SC5314 1356 20455
Ca21chr4_C_albicans_SC5314 11331 18001
Ca21chr6_C_albicans_SC5314 9856 100010

C. albicans SC5314 Assembly 19 example:
Contig19-10109 4600 24000
Contig19-10216 200310 220546

C. glabrata CBS138 example:
ChrA_C_glabrata_CBS138 3210 4513
ChrJ_C_glabrata_CBS138 16899 17037
mito_C_glabrata_CBS138 10000 10897

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 plus flanking sequences: bases upstream and bases downstream of each feature
Other data
CGD_Feature.tab file format)
gene_association file format)
S. cerevisiae and other Candida species Ortholog or Best hit

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