Prime User Manual - ISP

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Chapter 3: Prime–Structure Prediction: Initial Steps
3.1 Input Sequence Step
This step is used to read in an amino acid sequence from a file or from a protein structure in the
Workspace.
To read a sequence from a file:
• Click From File and specify a file containing the desired sequence.
Several file formats are supported, including FASTA, EMBL, GENBANK, and PIR. For a
complete list, see Appendix C. File formats are auto-detected by the program. Sequences
must be in standard uppercase one-letter code.
To read a sequence from the Workspace:
• Click From Workspace to read sequences from proteins in the Workspace.
If there are multiple chains with the same sequence, the sequence will be read in only
once.
After input, the Sequences table in the Step View area shows all available unique sequences
with their corresponding chain lengths in the order in which they are read. By default, the first
sequence read in is displayed in the sequence viewer in the upper section of the panel. If
multiple sequences have been read in, only one can be brought forward to the next step in a
given Prime run.
To select a query from the Sequences table:
• Click on a sequence to select it for this run.
This brings the selected sequence into the sequence viewer. The sequences are named by
extracting the name from either the PDB header or the FASTA file header. Non-unique
sequences are ignored. Non-unique names are modified to make them unique.
Note: Sequences longer than 1,000 residues generally include more than one domain. Divide
these sequences into probable domains and treat each domain as an individual query.
To continue:
• When you are satisfied with the query sequence, click Next to go to the Find Homologs
step.
If an error message appears when you click Next, you cannot proceed until the problem is
resolved. Error messages are listed in Appendix D. See Section D.1 on page 127 for help
with Input Sequence error messages.
Prime 2.1 User Manual