Delila Program: delila

delila program

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

{   version = 5.04; (* of delila.p 2017 Aug 09}

(* begin module describe.delila *)
   delila: the librarian for sequence manipulation

   delila(inst: in, book: out, listing: out,
          marksdelila: out,
          lib1: in, cat1: in,
          lib2: in, cat2: in,
          lib3: in, cat3: in,
          output: out, debug: out)

   inst: instructions written in the language delila that tell the
      program delila what sequences to pull out of the library.

   book: the set of sequences pulled out of the library.

   listing: the instructions are listed along with errors found or
      actions taken.

   marksdelila: Colored marks for the lister program that indicate
      the locations of base changes, insertions and deletions.

   lib1: the first library from which to obtain sequences
   cat1: the first catalogue, corresponding to lib1
   lib2: the second library
   cat2: the second catalogue, corresponding to lib2
   lib3: the third library
   cat3: the third catalogue, corresponding to lib3

   debug: traces through the actions taken, for debugging delila
      (only produced if variable debugging is true.)

   output: messages to the user


   Delila is a data base manager for nucleic acid sequences.  It takes a set
   of instructions, written in the language delila (DEoxyribonucleic acid
   LIbrary LAnguage) and a large set of sequences called a library.  The
   output is a listing of the actions taken (or errors) corresponding to the
   instructions, and a "book" containing the sequences desired.

   see the documentation

   libdef (defines delila), delman.intro, delman.use,

see also

   Definition of the database system:

   Introduction to Delila Instructions:

   Related programs:
   alist.p, catal.p, loocat.p, dbbk.p, lister.p

   dbmutate.p is deprecated: use the mutation method, 'with'

   ( )

   Thomas D. Schneider, Gary D. Stormo and Paul Morrisett
   useful suggestions by Jeff Haemer


   There used to be many known bugs in delila, related to extracting linear
   fragments of circular sequences.  Delila was rebuilt in the spring of 1999
   and is much more robust now.

   The following features are not available in this program:  recognition
   classes and enzymes, markers, automatic printing to the book of structures
   that intersect a piece, get all (for org, chr, rec and enz), get every and
   if.  The gene mechanism was revived on 2001 Mar 16, eventually it may be
   used to implement features.

   Delila programs use a packed array of bases.  This means that a smart
   Pascal compiler can store DNA sequences in two bits per base.  When delila
   was originally designed, I thought that everybody would complete their
   sequences and therefore there would never be unknown bases in a database.
   Silly me.  GenBank has plenty of such cases.  The dbbk program avoids this
   problem by converting such bases to 'a'.  Fortunately these can now be
   displayed with lister.  Someday Delila may be upgraded to handle this
   case, but it might be at the cost of reducing the maximum sequence that
   can be handled.

(* end module describe.delila *)
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