Various programs in the MEME Suite allow as input a file containing a multiple alignment of protein or DNA sequences. These input files must be in CLUSTAL W format (usually identified with the suffix ".aln").
The format is very simple:
Some rules about representing sequences:
* -- all residues or nucleotides in that column are identical
: -- conserved substitutions have been observed
. -- semi-conserved substitutions have been observed
-- no match.
Here is an example of a multiple alignment in CLUSTAL W format:
CLUSTAL W (1.82) multiple sequence alignment
FOSB_MOUSE MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA 60
FOSB_HUMAN MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA 60
************************************************************
FOSB_MOUSE ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS 120
FOSB_HUMAN ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPVVDPYDMPGTSYSTPGMSGYSSGGASGS 120
********************************.***************:*.**:******
FOSB_MOUSE GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT 180
FOSB_HUMAN GGPSTSGTTSGPGPARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT 180
****** ***** .**********************************************
FOSB_MOUSE DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD 240
FOSB_HUMAN DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD 240
************************************************************
FOSB_MOUSE LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY 300
FOSB_HUMAN LPGSAPAKEDGFSWLLPPPPPPPLPFQTSQDAPPNLTASLFTHSEVQVLGDPFPVVNPSY 300
****:.******.**************:*:**************************.***
FOSB_MOUSE TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL 338
FOSB_HUMAN TSSFVLTCPEVSAFAGAQRTSGSDQPSDPLNSPSLLAL 338
***********************:**************