Next: Defining the scoring Up: No Title Previous: Program limits

Defining a Pattern

The flexible pattern is defined around the block_file format described in APPENDIX II. The only additions necessary are if flexible gaps are to be included, when the following syntax is used.

>test  this is a test flexible pattern
>test2  this is also a flexible pattern
*iteration 1
ag                     each line in this file
vl <23:28              defines a pattern "ELEMENT"
ww <1:3
.     further pattern elements here



This file means: score against ag at position 1, vl at position 2 then allow between 23 and 28 gaps (inclusive) then score against pg, then ww, then allow a gap of 1 to 3 residues, then score kr etc etc.