make-na

Automation of making nucleic acid helices by NAB.

New make-na server!

Instructions

Using the make-na server should be intuitive. ASCII-art is used to depict duplexes and the server tries its best to infer what is meant by the depiction.

I have tried to put a lot of flexibility in duplex creation. A-, B-, and Z-DNA as well as A- and B-RNA. Z-RNA is not supported. If someone wants it, I'll try to add it. Mismatches are supported as well as uneven over-hangs and under-hangs. For example, these would all be valid ASCII-art duplexes:

  ATACCGATACGATAGAC
    TGGCTATGCTATCTGTA

      CGATACGATAGAC
    uGGCuAuGCuAuCuGuA

      ACTATAGGATACCAT
       GATAggCTATGGTA

Moreover, the program does its best to ignore comments and other mark-up, so the following will work just fine (the alignment of the two strands will be interpreted correctly):

     #   This is my favorite DNA.
     5' -    ATACCGATACGATAGAC    -3'
     3' -      TGGCTATGCTATCTGTA  -5'

Comments start with a "#" (preceeded by optional whitespace) and all non-alphabetic information is ignored on sequence lines, except for calculating alignment of the strands. Blank and whitespace only lines are ignored.

It is currently necessary to specifiy both strands, even if a blunt-ended canonical Watson-Crick helix is intended. This may change if I get enough requests.

If you have any suggestions or comments, feel free to contact me at .

© 2006 James Stroud. All rights reserved.
Revised April 23, 2006.