Delila Program: instal

instal program

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

{version = 1.49; (* of instal.p 1995 July 26}

(* begin module describe.instal *)
(*
name
      instal: delila instruction alignment

synopsis
      instal(xbook: in, ybook: in, shlist: in, inst: in,
             rinst: out, sinst: out, list: out, output: out)

files
      xbook: a delila system book containing one piece used to
         align the ybook pieces.
      ybook: a delila system book containing pieces to be aligned by
         the piece in xbook.
      shlist: the output of the sorth program.  these sorted helixes
         must have been generated using helix(xbook,ybook,hlist,...) and
         then sorth(hlist,shlist,...,[.../1/...]).  that is, sorth must
         have been used to select only the top 1 helix from hlist.
      inst: the instructions used to generate ybook (or a comparable set
         of instructions that correspond to the ones for ybook).
      rinst: reduced instructions: those instructions from inst that
         have a unique helix in shlist.  in other words, inst is copied to
         rinst only for instructions that have a unique alignment.
         the other instructions are also copied, but surrounded by
         comment delimiters to neutralize them.  neutrialized
         instructions are followed by a delila instruction that will
         maintain the original piece numbers.
      sinst: shifted instructions: the instructions written to rinst are
         realigned by the helixes of shlist.  the new alignment
         is the coordinate where the 5 prime end of the xpiece
         would lie on each y piece.
      list: progress of the realignemnt.
      output: messages to the user.

description
      the purpose of instal is to automatically realign a set of instructions.
      for example, if one has a set of instructions that define the
      initiation codon of some procaryotic ribosome binding sites,
      one may want another alignment by the shine and dalgarno.  to
      do this, the following steps are needed:
      1. the instructions (inst) are converted to a book (ybook) using
      delila.  instructions that define the 3 prime end of the 16s rrna are
      written and used to create xbook.
      2.  potential helixes between xbook and ybook are found with the
      helix program, making an hlist.
      3. the strongest helixes of the hlist are selected using the
      sorth program.  thus each piece of ybook has a unique (or no)
      helix associated with it.
      4. instal is used to alter the original instructions.  instructions
      (pieces) with no unique helix are neutralized by putting them in
      comments to in both rinst and sinst.  in addition, the instructions
      of sinst are 'shifted' so they are aligned by the 5 prime end of xpiece.

see also
      delila.p, helix.p, sorth.p

author
      thomas dana schneider

bugs
      none known

technical notes
      the largest shift that is recorded is specified by the
      constant absshift

*)
(* end module describe.instal *)
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