Supplementary material for RADAR-paper. 

The files are in gnu-zipped format.  

Please cite 

Heger A, Holm L. 2000. Algorithm for rapid automatic detection and 
alignment of repeats in protein sequences (RADAR) Proteins

when you use this material.

Andreas Heger

European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

Tel: +44 1223 494450
Fax: +44 1223 494468

Notes Section:

1. Header format in pfam.reference:

internal protein identifier # SWISS-PROT-ID # Pfam-information

where "Pfam-information" is a ';' separated list of
a) Pfam-Family
b) Pfam-ACC
c) Number of repeat units
d) dummy
e) average percent identity
f) average entroy

For example:
2cmcZce3wbap_amgsdi90a # FINC_BOVIN # Fibronectin; PF01770; 15;   24.11;    32.00;     1.99

2. Output format of RADAR:

The header contains the following fields:
a) Number of repeat units
b) total score = sum of all repeat unit scores
c) length of one repeat unit
e) offset of repeat diagonal
f) start residue of template repeat unit
g) end residue of template repeat unit
h) level of iteration. "Short" means that this repeat was found by
	the procedure for finding short conserved repeats.

Then follows the multiple alignment of repeat units in the format:
firstresidue-lastresidue (score, z-score) alignment

Lowercase characters correspond to unaligned positions. This means that this
residue was not aligned to the template repeat. '.' is used as a gap character.

For example:
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
            15|    1642.24|      88|      88|    1315|    1402|       1

File Section:

Created:	6.3.2000
Last updated:	6.3.2000

pfam.input.gz		identifiers and accession codes for sequences
				used in benchmarking RADAR
pfam.results.gz		results of benchmarking RADAR
pfam.reference.gz	reference alignments from Pfam

swiss.input.gz		identifiers and accession codes of proteins 
swiss.results.gz	results of scanning SWISS-PROT
novel.repeats.gz	filtered result set. All sequences with annotated 
				repeats in SWISS-PROT/Pfam and a score of 
				less than 60 have been removed