[rnafold] file *.connect ?

Jerry Learn learn at u.washington.edu
Tue Nov 24 13:49:16 EST 1998


In article <73dq12$nc2$2 at saphir.jouy.inra.fr>, lindenb at jouy.inra.fr
(Pierre Lindenbaum) wrote:

> hello world,
> 
> does anyone knows about the file *.connect created by the 'foldrna' program ?
> what do exactly represent the six columns ?
> 
> thank you for your help :-)
> 
> Pierre L.
> 
> (...)
> FOLDRNA of: _seq0.seq Check: 1763 from: 1 to: 100  October 9, 1998 14:47
> 
> 
> Length: 100  Energy: -28.2
>  ..
>     1 G       0    2   14    1
>     2 G       1    3   13    2
>     3 C       2    4   12    3
>     4 U       3    5   11    4
>     5 U       4    6    0    5
>     6 U       5    7    0    6
>     7 U       6    8    0    7
>     8 A       7    9    0    8
>     9 A       8   10    0    9
>    10 A       9   11    0   10
>    11 A      10   12    4   11
>    12 G      11   13    3   12
> (...)

I'll give this a try, although it's been a while.

column
   1     nucleotide number in model (i)
   2     nucleotide
   3     nucleotide number of the i-1th nucleotide (5' of i)
   4     nucleotide number of the 1+1th nucleotide (3' of i)
   5     nucleotide base-paired with nucleotide i
   6     nucleotide number label (does not have to equal i)

Close enough?
-- 
Jerry Learn <Learn at u.washington.edu>
U. of Washington 
Seattle, WA  98195-7740  USA      




More information about the Bio-soft mailing list