Delila Program: oligosetc

oligosetc program

Documentation for the oligosetc program is below, with links to related programs in the "see also" section.

{version = 1.03; (* of oligosetc.p 2000 Oct 2}

(* begin module describe.oligosetc *)
(*
name
   oligosetc: raw sequence to Oligo's Etc format

synopsis
   oligosetc(sequ: in, oligosetcp: in, order: out, output: out)

files
   sequ:  raw sequences with a, c, g, t and ending in "."

      If the first character of the first line of the file is
      a ">", then fasta format is assumed.  In this format
      the line following the ">" is the name of the next sequence.
      Sequences do not end in periods but rather with another ">"
      at the start of the line.
      The names will be printed to the order file.

   order:  multiple line detailed description of file 2, etc

   oligosetcp:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This allows the
         user to be warned if an old parameter file is used.

      modification (character):
         "5" means put an x on the 5' end to indicate 5' biotin
         "3" means put an x on the 3' end to indicate 3' biotin
         "8" means put an x on both the ends

      maxlinelength (integer):  maximum length of output lines.

   output: messages to the user

description
   Convert simple DNA sequence to the format that the Oligo's Etc company
   likes it in.  It is broken into sets of 3 bases with spaces between.  All
   bases are capitalized except g.  Biotins are indicated by X on the end.

examples

   sequ:

g gaattc aagctt
actcaaaaactgaacaac
cgggtcag
aagctt
g
c
gcgaagc
g
c
aagctt
ctgacccg
gttgttcagtttttgagt
aagctt gaattc c.

    gives:

oligo number 1

 5' ggA ATT CAA gCT TAC TCA AAA ACT gAA CAA CCg
ggT CAg AAg CTT gCg CgA AgC gCA AgC TTC TgA CCC
ggT TgT TCA gTT TTT gAg TAA gCT TgA ATT CC 3'

101 bases long

documentation

see also
   makebk.p

author
   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.oligosetc *)
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