Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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Chapter 11: Command Syntax<br />
The alignment file format is as follows. The first line corresponds to the query sequence (indicated<br />
by ProbeAA:) and the second line corresponds to the template sequence (indicated by<br />
Fold AA:). A period is used as a gap character, and an X is used for non-standard residues.<br />
Below is a sample alignment file.<br />
ProbeAA: .AAEEKTEFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESA...PAALKEGVSKDDAEALKKALEEAG<br />
AEVEVK<br />
Fold AA: AAQEEKTEFDVVLKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAG<br />
AEVELK<br />
The sequences are split for formatting reasons, and should be on a single line in the actual file.<br />
11.3 fr—Fold Recognition<br />
fr finds template proteins that are similar to the query sequence at both sequence and structure<br />
levels.<br />
The fold recognition program used in <strong>Prime</strong> differs from standard sequence search program<br />
such as BLAST by taking into account secondary structure matching and profile-sequence<br />
matching. As a result, fr can find structural homologs with low sequence identity to the query<br />
(
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