remap.txt

emboss的linux版本的源代码

                                   remap 



Function

   Display sequence with restriction sites, translation etc

Description

   The Restriction Enzyme database (REBASE) is a collection of
   information about restriction enzymes and related proteins. It
   contains published and unpublished references, recognition and
   cleavage sites, isoschizomers, commercial availability, methylation
   sensitivity, crystal and sequence data. DNA methyltransferases, homing
   endonucleases, nicking enzymes, specificity subunits and control
   proteins are also included. Most recently, putative DNA
   methyltransferases and restriction enzymes, as predicted from analysis
   of genomic sequences, are also listed.

   The home page of REBASE is: http://rebase.neb.com/

   This program uses REBASE data to find the recognition sites and/or cut
   sites of restriction enzymes in a nucleic acid sequence.

   This program displays the cut sites on both strands by default. It
   will optionally also display the translation of the sequence.

   There are many options to change the style of display to aid in making
   clear presentations.

   One potentially very useful option is '-flatreformat' that displays
   not only the cut sites which many other restriction cut-site programs
   will show, but also shows the recognition site.

   By default, only one of any group of isoschizomers (enzymes that have
   the same recognition site and cut positions) is reported (this
   behaviour can be turned off by setting the qualifier '-limit' to be
   false.) The reported enzyme from any one group of isoschizomers (the
   prototype) is specified in the REBASE database and the information is
   held in the data file 'embossre.equ'. You may edit this file to set
   your own preferred prototype,if you wish.

   As well as the display of where enzymes cut in the sequence, remap
   displays:

     * The list of enzymes that cut the sequence and match the required
       criteria.
     * The list of enzymes that cut the sequence and fail the MINCUTS
       criteria.
     * The list of enzymes that cut the sequence and fail the MAXCUTS
       criteria.
     * The list of enzymes that do not cut the sequence but which match
       all the required criteria.
     * The number of enzymes that cut the sequence and fail the SITELEN,
       BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria.

Usage

   Here is a sample session with remap

   This example uses only a small region of the input sequence to save
   space. This is run with a small test version of the restriction enzyme
   database and so you will probably see more enzymes when you run this.


% remap -notran -sbeg 1 -send 60 
Display sequence with restriction sites, translation etc.
Input nucleotide sequence(s): tembl:eclac
Comma separated enzyme list [all]: taqi,bsu6i,acii,bsski
Minimum recognition site length [4]: 
Output file [eclac.remap]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   This is an example where all enzymes in the REBASE database are used,
   (but only the prototypes of the isoschizomers are reported by
   default). This is run with a small test version of the restriction
   enzyme database and so you will probably see more enzymes when you run
   this.


% remap -notran -sbeg 1 -send 60 
Display sequence with restriction sites, translation etc.
Input nucleotide sequence(s): tembl:eclac
Comma separated enzyme list [all]: 
Minimum recognition site length [4]: 
Output file [eclac.remap]: 

   Go to the output files for this example

   Example 3

   This is an example where all enzymes in the REBASE database are used
   but the -limit qualifier is not set so that all of the enzymes are
   displayed and not just only the prototypes of the isoschizomers. This
   is run with a small test version of the restriction enzyme database
   and so you will probably see more enzymes when you run this.


% remap -notran -sbeg 1 -send 60 -nolimit 
Display sequence with restriction sites, translation etc.
Input nucleotide sequence(s): tembl:eclac
Comma separated enzyme list [all]: 
Minimum recognition site length [4]: 
Output file [eclac.remap]: 

   Go to the output files for this example

   Example 4

   This shows the 'flat' format: This is run with a small test version of
   the restriction enzyme database and so you will probably see more
   enzymes when you run this.


% remap -notran -sbeg 1 -send 60 -flat 
Display sequence with restriction sites, translation etc.
Input nucleotide sequence(s): tembl:eclac
Comma separated enzyme list [all]: 
Minimum recognition site length [4]: 
Output file [eclac.remap]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -enzymes            string     [all] The name 'all' reads in all enzyme
                                  names from the REBASE database. You can
                                  specify enzymes by giving their names with
                                  commas between then, such as:
                                  'HincII,hinfI,ppiI,hindiii'.
                                  The case of the names is not important. You
                                  can specify a file of enzyme names to read
                                  in by giving the name of the file holding
                                  the enzyme names with a '@' character in
                                  front of it, for example, '@enz.list'.
                                  Blank lines and lines starting with a hash
                                  character or '!' are ignored and all other
                                  lines are concatenated together with a comma
                                  character ',' and then treated as the list
                                  of enzymes to search for.
                                  An example of a file of enzyme names is:
                                  ! my enzymes
                                  HincII, ppiII
                                  ! other enzymes
                                  hindiii
                                  HinfI
                                  PpiI (Any string is accepted)
   -sitelen            integer    [4] This sets the minimum length of the
                                  restriction enzyme recognition site. Any
                                  enzymes with sites shorter than this will be
                                  ignored. (Integer from 2 to 20)
  [-outfile]           outfile    [*.remap] Output file name

   Additional (Optional) qualifiers:
   -mincuts            integer    [1] This sets the minimum number of cuts for
                                  any restriction enzyme that will be
                                  considered. Any enzymes that cut fewer times
                                  than this will be ignored. (Integer from 1
                                  to 1000)
   -maxcuts            integer    [2000000000] This sets the maximum number of
                                  cuts for any restriction enzyme that will
                                  be considered. Any enzymes that cut more
                                  times than this will be ignored. (Integer up
                                  to 2000000000)
   -single             boolean    [N] If this is set then this forces the
                                  values of the mincuts and maxcuts qualifiers
                                  to both be 1. Any other value you may have
                                  set them to will be ignored.
   -[no]blunt          boolean    [Y] This allows those enzymes which cut at
                                  the same position on the forward and reverse
                                  strands to be considered.
   -[no]sticky         boolean    [Y] This allows those enzymes which cut at
                                  different positions on the forward and
                                  reverse strands, leaving an overhang, to be
                                  considered.
   -[no]ambiguity      boolean    [Y] This allows those enzymes which have one
                                  or more 'N' ambiguity codes in their
                                  pattern to be considered
   -plasmid            boolean    [N] If this is set then this allows searches
                                  for restriction enzyme recognition site and
                                  cut postions that span the end of the
                                  sequence to be considered.
   -[no]commercial     boolean    [Y] If this is set, then only those enzymes
                                  with a commercial supplier will be searched
                                  for. This qualifier is ignored if you have
                                  specified an explicit list of enzymes to
                                  search for, rather than searching through
                                  'all' the enzymes in the REBASE database. It
                                  is assumed that, if you are asking for an
                                  explicit enzyme, then you probably know
                                  where to get it from and so all enzymes
                                  names that you have asked to be searched
                                  for, and which cut, will be reported whether
                                  or not they have a commercial supplier.
   -table              menu       [0] Genetic code to use (Values: 0
                                  (Standard); 1 (Standard (with alternative
                                  initiation codons)); 2 (Vertebrate
                                  Mitochondrial); 3 (Yeast Mitochondrial); 4
                                  (Mold, Protozoan, Coelenterate Mitochondrial
                                  and Mycoplasma/Spiroplasma); 5
                                  (Invertebrate Mitochondrial); 6 (Ciliate
                                  Macronuclear and Dasycladacean); 9
                                  (Echinoderm Mitochondrial); 10 (Euplotid
                                  Nuclear); 11 (Bacterial); 12 (Alternative
                                  Yeast Nuclear); 13 (Ascidian Mitochondrial);
                                  14 (Flatworm Mitochondrial); 15
                                  (Blepharisma Macronuclear); 16
                                  (Chlorophycean Mitochondrial); 21 (Trematode
                                  Mitochondrial); 22 (Scenedesmus obliquus);
                                  23 (Thraustochytrium Mitochondrial))
   -frame              menu       [6] This allows you to specify the frames
                                  that are translated. If you are not
                                  displaying cut sites on the reverse sense,
                                  then the reverse sense translations will not
                                  be displayed even if you have requested
                                  frames 4, 5 or 6. By default, all six frames
                                  will be displayed. (Values: 1 (1); 2 (2); 3
                                  (3); F (Forward three frames); -1 (-1); -2
                                  (-2); -3 (-3); R (Reverse three frames); 6
                                  (All six frames))
   -[no]cutlist        boolean    [Y] This produces lists in the output of the
                                  enzymes that cut, those that cut but are
                                  excluded because that cut fewer times than
                                  mincut or more times than maxcut and those
                                  enzymes that do not cut.
   -flatreformat       boolean    [N] This changes the output format to one
                                  where the recognition site is indicated by a
                                  row of '===' characters and the cut site is
                                  pointed to by a '>' character in the
                                  forward sense, or a '<' in the reverse sense
                                  strand.
   -[no]limit          boolean    [Y] This limits the reporting of enzymes to
                                  just one enzyme from each group of
                                  isoschizomers. The enzyme chosen to
                                  represent an isoschizomer group is the
                                  prototype indicated in the data file
                                  'embossre.equ', which is created by the
                                  program 'rebaseextract'. If you prefer
                                  different prototypes to be used, make a copy
                                  of embossre.equ in your home directory and
                                  edit it. If this value is set to be false
                                  then all of the input enzymes will be
                                  reported. You might like to set this to
                                  false if you are supplying an explicit set
                                  of enzymes rather than searching 'all' of
                                  them.

   Advanced (Unprompted) qualifiers:
   -[no]translation    boolean    [Y] This displays the 6-frame translations
                                  of the sequence in the output.
   -[no]reverse        boolean    [Y] This displays the cut sites and
                                  translation of the reverse sense.
   -orfminsize         integer    [If this value is left as 0 then all of the
                                  translation is shown.] This sets the minimum
                                  size of Open Reading Frames (ORFs) to
                                  display in the translations. All other
                                  translation regions are masked by changing
                                  the amino acids to '-' characters. (Integer
                                  0 or more)
   -uppercase          range      [If this is left blank, then the sequence
                                  case is left alone.] Regions to put in
                                  uppercase.
                                  If this is left blank, then the sequence
                                  case is left alone.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are separated by any non-digit,
                                  non-alpha character.
                                  Examples of region specifications are:
                                  24-45, 56-78
                                  1:45, 67=99;765..888
                                  1,5,8,10,23,45,57,99
   -highlight          range      [(full sequence)] Regions to colour if
                                  formatting for HTML.
                                  If this is left blank, then the sequence is
                                  left alone.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are followed by any valid HTML font
                                  colour.
                                  Examples of region specifications are:
                                  24-45 blue 56-78 orange
                                  1-100 green 120-156 red
                                  A file of ranges to colour (one range per
                                  line) can be specifed as '@filename'.
   -threeletter        boolean    [N] Display protein sequences in
                                  three-letter code
   -number             boolean    [N] Number the sequences
   -width              integer    [60] Width of sequence to display (Integer 1
                                  or more)
   -length             integer    [0] Line length of page (0 for indefinite)
                                  (Integer 0 or more)
   -margin             integer    [10] Margin around sequence for numbering
                                  (Integer 0 or more)
   -[no]name           boolean    [Y] Set this to be false if you do not wish
                                  to display the ID name of the sequence
   -[no]description    boolean    [Y] Set this to be false if you do not wish
                                  to display the description of the sequence
   -offset             integer    [1] Offset to start numbering the sequence
                                  from (Any integer value)
   -html               boolean    [N] Use HTML formatting

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide