IUBio

[rnafold] file *.connect ?

Rick Westerman westerm at postoffice.purdue.edu
Tue Nov 24 17:19:03 EST 1998


> does anyone knows about the file *.connect created by the rnafold program ?
> what do exactly represent the six columns ?
>...
>     1 G       0    2   14    1
>     2 G       1    3   13    2

As I recall, the columns are:

   1) The relative number of the base (nucleoside) inside the sequence
   2) The base
   3) What base number does the current base connect to, downstream
   4) Ditto, but for upstream

Note:  Ok, columns 3 & 4 are rather redundent!

   5) What base does the current base pair to; i.e., what does it fold
with?
   6) The absolute base number.

Note: Columns 1 and 6 are often the same, however if you told the
program to start folding at base #80 (for example) the column 1, row 1
would be "1" and column 6, row 1 would be "80"

Hope this helps.

-- Rick

Rick Westerman                System Manager of the Ag Campus Lab. for
westerm at purdue.edu            Computational Biology (ACLCB) & Sys. Mgr.
Phone: (317) 494-0505         of the Biochemistry department BCHM bldg.  
  FAX: (317) 494-7897         Purdue Univ. W. Lafayette, IN 47907
href="http://www.biochem.purdue.edu/~westerm"



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