Delila Program: dashseq

dashseq program

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

{   version = 1.00; (* of dashseq.p 2010 Nov 21}

(* begin module describe.dashseq *)
(*
name
   dashseq: convert aligned sequences with dashes to pure sequences

synopsis
   dashseq(dashedseq: in, dashseqp: in, sequ: out, output: out)

files

   dashedseq:  Aligned DNA sequences, one per line.
      The first one is the 'cononical sequence and it may not contain
      any dashes.
      The following lines are copied to the sequ output except when
      there is a dash, it is replaced by the corresponding letter
      in the canonical sequence.

   sequ:  pure sequence without dashes.

   dashseqp:  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.

      not used yet.

   output: messages to the user

description

   Sometimes sequnces are given with dashes to indicate that the letter
   is the same as the letter in a cononical

examples

documentation

Examples are in figures 2 and 3 of:

@article{Argast.Monnat1998,
author = "G. M. Argast
 and K. M. Stephens
 and M. J. Emond
 and R. J. {Monnat Jr}",
title = "{I-\emph{PpoI} and I-\emph{CreI} homing site sequence
degeneracy determined by random mutagenesis and sequential \emph{in
vitro} enrichment}",
journal = "J Mol Biol",
volume = "280",
pages = "345--353",
pmid = "9665841",
year = "1998"}

see also

author

   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.dashseq *)
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