Follow the steps below to run the BLASTP program, which performs a protein versus protein comparison.

  1. View the details form for some gene:

  1. Click the Protein tab.
  2. Click Run BLAST... button. The Run BLAST window displays.
  3. The Sequence text box will be populated with the protein sequence of the selected gene model.


The FASTA header line is optional if only one sequence is used as a query. In case of multiple query sequences each of them should have the FASTA header. The identifier from the header will be shown in the Query column of the blast results window, so please keep the identifiers unique.

  1. In the Program panel check (select) the BLASTP radio button.
  2. From the map set tree panel, select the subject collection of proteins to use for search. As the subject data set, BLASTP will use a collection of proteins generated from the gene models predicted by selected method. If a map set has several gene model tracks predicted by different methods, under the map set node of the tree you will see several check boxes - one for each of the methods.
  3. Check (select) the Fast or Normal radio button in the Sensitivity/Speed panel.


The Primer option is grayed out since it is not a valid option for BLASTP.

  1. If the provided default parameters need modification, please check the "Override arguments" box in the Advanced panel. Please note, there is a "?" button that opens the help page with the list and description of BLAST parameters.
  2. Click OK to run. The BLAST in Progress window displays.
  3. When the BLAST process finishes, the BLAST Results window displays. See BLAST Results Window for details.