Specifying query sequence

In PFMFind terminology, an experiment consists of an annotated protein sequence that serves as a source of query fragments together with associated search results. Exactly one experiment must be active in order to run searches and examine search results. Experiments are created and set active through the Experiment tab.

PFMFind Experiment tab

Experiment tab

Experiment tab consists of two panels: Experiments and Query sequence. The Experiments panel shows all available experiments, while the Query sequence panel displays the sequence associated with the current experiment.

Creating a new experiment

  • Click the New button. The boxes for entering data will become enabled.
  • Enter - Experiment name in the entry field above the list (Experiments panel). This will be used to identify experiment in the list. - Experiment description in the Description box (Experiments panel). - Sequence description in the Description box (Query sequence panel). - Protein sequence in the Sequence box (Query sequence panel).
  • Click the Update button to enter the experiment into the database.


The experiment description can be changed/updated at any time. Hence, it can serve to store the notes about the searches performed. After editing, click the Update button to save the changes. The other three fields cannot be changed after they are saved.

Setting the current experiment

  • Select an experiment by highlighting it in the list in the Experiments panel.
  • Click the Set button. The selected experiment will become current.


Pressing the Set button when the current experiment is selected in the list unsets the current experiment.

Uploading query sequences as a batch

  • Click Upload from file button.
  • Select a file in FASTA format.
  • PFMFind will automatically construct experiments by uploading all sequences from that file. Experiment names will be formed by concatenating the name of the file and the sequenctial number of the correpsonding protein sequence.

Deleting an experiment

Click the Delete button. You will get a confirmation dialog.