BMERC : needle tools : Introduction : Threading alignment results

[Should be part of a much larger set of needle documentation, but, alas, I haven't been keeping this up. -- rgr, 15-Sep-99.]

Table of Contents

1. Threading alignment experiments
   1. Table of Contents
   2. Running threading alignment experiments
   3. Grading threading alignment results
      1. Grading cross-threadings using ctimaps
      2. Grading cross-threadings using alignments

[document the timing-kludge-cross-predict-list function, "timing file" format. -- rgr, 15-Sep-99.]

Grading threading alignment results

Grading cross-threadings is harder, since it requires an external definition of which sequence residues belong in which core positions. Historically, this has been provided in two ways. The first technique uses a mapping between the core positions of the threaded core and a core made from the threaded sequence. This mapping was produced from an FSSP alignment by the fssp-core-corr.pl program. Although this technique suffers from the fact that one must be able to build a core for the sequence, and that only residues that appear in the core in both structures can be scored, it is still supported for backward compatibility.

The second technique for grading cross-threadings uses the FSSP alignment file directly, and hence can be done for such things as sequence regular expressions that can have no core structure.

Grading cross-threadings using ctimaps