Download a Protein Input File Template

[Admin Home]

Download a Protein Input File Template By either file or text area, input a series of proteins on separate lines, with each line containing the protein name, followed by a tab, followed by the species. Please be patient as it could take a while!

The following fields will still require you to fill them in manually, and will indicate so in the template file:

JASPAR ID
DNA binding domain(s)
Unique species-based id (if applicable)
"Has PBM data" field (see instructions on previous page)

The script is somewhat error-prone in the following ways:

It may fail to find appropriate UniProt or RefSeq accession #s.
RefSeq: The script may not choose the accession number corresponding to the appropriate isoform.
UniProt: The script may choose a TrEMBL-based accession number over the preferred SwissProt number when both are available; SwissProt tends to have more comprehensive information and provide good protein description, which we use to fill the "description" field when available.
An empty (NULL) description field is thus often a sign of inappropriate UniProt ID selection.

You should check over your file for potential errors and manually insert the correct information yourself.

The tab-delimited input file may be hard to read. Here is a helpful script which will cleanly parse the file for human readability, to help you spot potential errors. It will print to the console by default, so on a Unix-based system use ">" to write to a file.

File:

Text area:

Email: