DAF format for a list of pairs

(search with one sequence U against a database)

The following file contains only the compulsory (bold) and recommended elements of a valid DAF format for presenting an aligned pair. Note the following:

Keywords are mandatory (ALISYM, NPAIRS, idSeq, idStr, lenSeq, lenStr, seq, str).
Lines starting with # and no keyword will be ignored.
Columns are separated by tabs or blanks.
For a simple rank analysis you can skip the sequences.

Notation:

'seq' = sequence of search sequence U,

'str' = sequence of database protein.

# DAF (dirty alignment format for exchange with Aqua)
# ALISYM	ACDEFGHIKLMNPQRSTVWY.acdefghiklmnpqrstvwy
# NPAIRS	3
# ALIGNMENTS

idSeq	idStr	lenSeq	lenStr	lenAli	pide	seq	str
1acf	2btfP	125	513	19	17	SWQTYVDTNLVGTGAVTQ	GWNAYID.NLMADGTCQD
1acf	2btf	125	513	21	17	SWQTYVD...VGTGAV..	GGMINKKCYEMASHLRRSQY
1acf	1asu	125	513	19	17	SWQTYVDTNLVGTGAVTQ	PLQIWQTDFTLAVTVDTA