ooooooooxxxxoooooooo

ooooooooxxxxoooooooo
ooooooooxxxxoooooooo
ooooooooxxxxoooooooo
ooooooooxxxxoooooooo
ooooooooxxxxoooooooo
ooooooooxxxxoooooooo
ooooooooxxxxoooooooo
Columns defined
ooooooooxxxxoooooooo by a preliminary
ooooooooxxxxoooooooo alignment of the
sequences
provide initial
estimates of
frequencies of
amino acids in
each motif
column

Columns not in motif provide

background frequencies
Sequence 1 xxxxoooooooooooooooo
xxxx
A

oxxxxooooooooooooooo
xxxx
B

ooxxxxoooooooooooooo
xxxx
C

Use previous ...background

estimates of amino frequencies in the
acid frequencies for remaining positions.
each column in the
motif to calculate
probability of motif in
this position, and
multiply by...
The resulting score gives the likelihood that the motif
matches positions (a) 1-20, (b) 6-25, or (c) 11-30 in sequence 1.
Repeat for all other positions and find most likely
locator. Then repeat for the remaining sequences.
 Motif

xxxMxxxxxx xxxMxxxxxx
xxxxxxMxxx xxxxxxMxxx
xxxxxMxxxx xxxxxMxxxx
xMxxxxxxxx xMxxxxxxxx
xxxxxxxxxM xxxxxxxxxM
Mxxxxxxxxx Mxxxxxxxxx
xxxxMxxxxx xxxxMxxxxx
xMxxxxxxxx xMxxxxxxxx
xxxxxxxxMx xxxxxxxxMx
Random start Location of motif in each
positions chosen sequence provides first
estimate of motif composition