Delila Program: meri

meri program

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

{   version = 1.12; (* of meri.p 2011 Feb 08}

(* begin module describe.meri *)
(*
name
   meri: merge ribl files

synopsis
   meri(ribl5, ribl3: in, merip: in, ribl53: out, output: out)

files

   ribl5, ribl3:  multiple line detailed description of the first file.

   ribl53:  multiple line detailed description of the second file.

   merip:  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.

      ribl53name (string): name of the new matrix.  However, if the
      first string on the line is '+', then the name is made by fusing
      the  names of the ribl5 and ribl3.

      ribl5from and ribl5to (integer): from and to locations of the 5'
         ribl to use.

      ribl3from and ribl3to (integer): from and to locations of the 3'
         ribl to use.

      zero (integer): new zero coordinate on the 5' ribl coordinate system.
         This is counted from the 5' end (as 1)

   output: messages to the user

description

   Merge two ribl weight matricies together.  The upstream one is
   called the 5' and the downstream one is called the 3'.

examples

   Fuse the donor splice site (-3 to +6) on the 5' end to the acceptor
   splice site (-25 to +2) on the 3' end by taking the intron side.
   By our original definition, the zero base is the one on the intron
   side, so the zero coordinates are removed to give numbering:

   -3 -2 -1       from donor
            +1 +2 from acceptor
   -2 -1  0 +1 +2 new numbering using position 3 as the new zero

   The merip parameter file for this is:

1.00  version of meri that this parameter file is designed for.
doac  ribl53name: string name of the merged ribl
-3 -1 ribl5from, ribl5to: range to use from the 5' ribl
+1 +2 ribl3from, ribl3to: range to use from the 3' ribl
3     zero (integer): new zero coordinate on the 5' ribl coordinate system.

documentation

@article{Stephens.Schneider1992,
author = "R. M. Stephens
  and T. D. Schneider",
title = "Features of spliceosome evolution and function
inferred from an analysis of the information at human splice sites",
journal = "J. Mol. Biol.",
volume = "228",
pages = "1124-1136",
note = "\htmladdnormallink
{http://alum.mit.edu/www/toms/papers/splice/}
{http://alum.mit.edu/www/toms/papers/splice/}",
year = "1992"}

see also

author

   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.meri *)
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