[EMBOSS] use water/matcher to find where RNA bybridizes

[Guy Bottu]

from : Belgian EMBnet Node

	Dear colleagues,

One of our users had a problem : how to find the location where a small 
molecule of RNA binds to a mRNA and so interferes with its functioning. 
Nothing in EMBOSS and nothing found on the WWW. We finally did the 
following : use revseq -nocomp to reverse the mRNA and then align the two 
sequences using as matrix :
-------------------------------
    A   T   G   C   S   W   R   Y   K   M   B   V   H   D   N   U
A   0   5   0   0   0   5   5   0   0   5   0   5   5   5   5   0
T   5   0   5   0   0   5   0   5   5   0   5   0   5   5   5   5
G   0   5   0   5   5   0   5   0   5   0   5   5   0   5   5   3
C   0   0   5   0   5   0   0   5   0   5   5   5   5   0   5   0
S   0   0   5   5   5   0   5   5   5   5   5   5   5   5   5   0         
W   5   5   0   0   0   5   5   5   5   5   5   5   5   5   5   5
R   5   0   5   0   5   5   5   0   5   5   5   5   5   5   5   0
Y   0   5   0   5   5   5   0   5   5   5   5   5   5   5   5   5
K   0   5   5   0   5   5   5   5   5   0   5   5   5   5   5   5
M   5   0   0   5   5   5   5   5   0   5   5   5   5   5   5   0          
B   0   5   5   5   5   5   5   5   5   5   5   5   5   5   5   5   
V   5   0   5   5   5   5   5   5   5   5   5   5   5   5   5   0
H   5   5   0   5   5   5   5   5   5   5   5   5   5   5   5   5
D   5   5   5   0   5   5   5   5   5   5   5   5   5   5   5   5
N   5   5   5   5   5   5   5   5   5   5   5   5   5   5   5   5
U   0   5   3   0   0   5   0   5   5   0   5   0   5   5   5   5
-------------------------------
This gave a reasonable result. water made the following alignment :
------------------------------
#=======================================
#
# Aligned_sequences: 2
# 1: mRNA
# 2: RNAi
# Matrix: HYB
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 49
# Identity:       3/49 ( 6.1%)
# Similarity:     0/49 ( 0.0%)
# Gaps:           0/49 ( 0.0%)
# Score: 185.0
# 
#
#=======================================

mRNA            2892 AATGTTGTGTGAGGATAATAGTAATAGTAATAGTAATAATAATAATAAT  2940
                     ..  . . .... ... .. .. .. .. ..  ................
RNAi               1 TTTGACCCTGCTACTACTACTACTACTACTACGATTATTATTATTATTA  49
--------------------------------
The only thing which bothers me is that the base pairs (which do have a 
positive comparison score) are not labeled as "similar", they get a '.' 
instead of a ':'. Does someone know why this is ?

	Guy Bottu