For example, start with a list of protein sequence identifiers → find the corresponding gene identifiers:

1: INPUT

• Prepare a file that lists the unique identifiers (UIDs) of records from a source database (for example, protein sequence identifiers), one UID per line, up to 100,000 UIDs maximum (sample file). The UIDs should be integers only (i.e., use GI numbers, not accession numbers), and the current range of acceptable is 0 to 4294967295. The FLink help document provides additional details about valid UIDs.



• Open the FLink search page.



• Open the "Please choose a database to start" menu and select the item that represents your source database (in this example, "Protein").



• Select "Upload ID List," use the "Browse" function to find your file, then press "Submit."

2: REVIEW input & select destination database

• FLink will display a "Protein" folder tab that provides a summary view of your input items, including descriptive information that FLink obtained from the Entrez Protein database for each of the input items. The folder tab lists the proteins in order of increasing UID, regardless of the order in which they were input into the system, and ignores duplicate UIDs.



• Click on the "LinkTo" function in the folder tab to open a dialog box that lists the possible destination databases and link types you can select. Click on an option to view its description in the dialog box. When you find an option of interest to you, for example, protein_gene, select it and press "Submit."

3: OUTPUT - expand job summary panel, then select "DOWNLOAD ONE-TO-ONE MAPPING IN CSV"

• The resulting output page will display a job summary (e.g., "Links from protein records to gene records weighted by frequency (click to see details)," followed by a "Gene" folder tab displaying a ranked ("frequency-weighted") list of the genes that are linked to the proteins from your input list.



• Click on the job summary title to expand that panel and see more details.



• Click on "download one-to-one mapping in csv" in the "Link method" section of the job summary panel. This is an alternative output format that allows you to download the underlying link data in raw form, grouped by the UID of input items rather than sorted as a frequency-weighted list.



• Note that some items from your input list might not have any links to items in the destination database. The csv file will only include UIDs from your input list that have links to at least one item in the selected destination database. If an item from your input list has links to multiple items in the destination database, each pairwise linkage will be listed on a separate row of the csv file.

(Tip: The URL at the top of the output page will show the Job ID for that particular LinkTo operation. You can save the URL and use it anytime during the next 24 hours to view your results again.)