Specification of DAF format

Purpose:

communication with AQUA (assessment of alignment quality)
computer parsable/human editable format for pairwise alignments

In the following you'll find a commented version of the DAF format including all compulsory, recommended, and optional elements. For simplicity you can find examples for DAF files containing the compulsory and recommended information, only:

one pair ,
a list of pairs (search with one sequence U against a database),
a list of lists of pairs (search with a number of test set sequences {U} against a database).

Overview over document:

compulsory elements,
recommended elements,
optional elements.
full file with all elements being clickable.

Features of DAF format:

Only the first pair with identical identifiers is taken.
If you don't provide the length of the proteins, the output will list them as equal to 1.
Larger z-scores are expected to reflect more reliable predictions.

Possible DAF file with explanations

All format elements (keywords, and entire lines) in boldface.

# DAF           	(dirty alignment format)
#
#	information:	
#			1) in all lines not beginning with '#'
#			2) in lines beginning with '#' and a keyword 
#			   (e.g.: ALISYM, NPAIRS, NSEARCH, ALIGNMENTS)
#	comments:	lines beginning with '#'
#	rows:		one line per pair alignment
#	columns:	separated by tabs or blanks (succession not important)
#	
#	purpose:	communicating pair alignments to Aqua (Alignment QUality Assessment)
#       
#	note 1:		If you give only id's (no alignmentss) AQUA will perform
#			an analysis of rank correlations, only.
#	note 2:		Please use the keywords given in this example
# 
# 
# SOURCE:	/data/hssp/1atf.hssp
# ALISYM:	ACDEFGHIKLMNPQRSTVWY.
# NPAIRS:	5 (or (for test sets: 2,3)
# NSEARCH:	1
# ADDKEYS:	addMy1,addMy2 
# 
#	note 3:		Additional column names that can be interpreted
#			by AQUA are: 'conf', 'zDali', 'rmsDali' for the presentation
#			of the true alignments.
# 
# 
# RELKEYS:	zMy1,zMy2
# RELHISTO:	3,2,1
# 
# ALIGNMENTS

idSeq	idStr	rank	conf	lenSeq	lenStr	lenAli	pide	seq	str	weightSeq
1acf	2btfP	1	9	125	513	19	17	SWQTYVDTNLVGTGAVTQ	GWNAYID.NLMADGTCQD	1111111111111111111111
1acf	2btf	2	9	125	513	21	17	SWQTYVD....GTGAVTQ	GG..NKKCYEMASHLRRSQY	111111222211111111111222
1acf	1asu	3	9	125	513	19	17	SWQTYVDTNLVGTGAVTQ	PLQIWQTDFTLAVTVDTA
9rnt	1gmp	1	9	104	193	20	17	GSNaYSSSDVSTAQAAGYK	VSGTVCLSALPPEATDTLN
9rnt	1srp	2	9	104	468	20	15	GSNaYSSSDVSTAQAAGYK	GGH.YAAAPLLDDIAAIQH

Compulsory elements

# DAF # ALIGNMENTS

idSeq idStr
1acf 2btfP

Recommended elements

# ALISYM ACDEFGHIKLMNPQRSTVWY.acdefghiklmnpqrstvwy # NPAIRS 1

lenSeq lenStr lenAli pide seq str
125 513 19 17 SWQTYVDTNL...GAVTQ GWNAYID.NLMADGTCQD

Optional elements

# SOURCE: /data/hssp/1atf.hssp # NSEARCH: 1 # ADDKEYS: addMy1,addMy2 # RELKEYS: zMy1,zMy2 # RELHISTO: 3,2,1

rank conf zscore zDali rmsDali weightSeq
1 9 3.2 16.8 2.1 111111112222111511111
3 2 2.2 3.8 6.1 111199111111