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# --force option in hybrid

Tue, 03/13/2012 - 04:46

y_kim2

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Joined: 03/13/2012

I am using hybrid or hybrid-min with --force option.

What I would like to calculate is the free energy of 3'end-anchored hybridization (3'end 3base exact match).

Suppose the length of the input sequence is n, that can be calculated as

"hybrid --force (n-2),0,3 (sequence_1) (sequence_2)"

or

"hybrid --force 0,n,3 (sequence_2) (sequence_1)"

I was thinking those two give the same results.

However, the both commands produced different results.

So I would like to ask if my understanding is correct.

Thanks in advance.

Your understanding is not correct. The command

`hybrid(-min) --force=(n-2),0,3 (sequence_1) (sequence_2)`

would force the last three bases of the first sequence to hybridize with

anythree bases of the second sequence. The choice of the bases would be determined by the program to minimize free energy. The notation`--force i,j,k`

forces the base pairs i-j, (i+1)-(j-1)..., (i+k-1)-(j-k+1). Note that in the base pair i-j, i is the base number in the first sequence and j is the base number in the second sequence. If j = 0, then bases i, i+1, ... i+k-1 of the first sequence must form base pairs with someprogram chosenbases of the second sequence. If i = 0, then bases j, j-1, ... j-k+1 of the second sequence must form base pairs with someprogram chosenbases of the first sequence.Suppose that the sequences are

1: 5'-tcgactacggactggcgatctacgcgagctatcgagctacgctACG-3' and

2: 5'-tcgactacggactggcgatctacgcgagctatcgagctacgctCGT-3'

Both have length 46 (n = 46 for both). Then running

`hybrid-min`

with`--force=44,0,3`

givesRunning

`hybrid-min`

with`--force=--force=0,46,3`

givesRunning

`hybrid-min`

with`--force=44,46,3`

givesDo you understand?

I have an important comment to add. By not specifying RNA or DNA, you got the default, which is RNA. The free energies are for RNA using the old version 2.3 free energies at 37 °C. If you are simulating DNA hybridization, then you must use

`--NA=DNA`

. If you specify no temperature, 37 °C will be used by default. It isalmost alwaysbetter to specify everything on a command line rather than to rely on default values. Run`hybrid(-min) -h`

for details and/or look at the man pages.