
                                   remap 
                                      
   
   
Function

   Display a sequence with restriction cut 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   contains published and unpublished references, recognition and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.
   
Usage

   Here is a sample session with remap
   
   This example uses only a small region of the input sequence to save
   space.
   

% remap -notran -sbeg 1 -send 60 
Display a sequence with restriction cut sites, translation etc..
Input 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:
   

% remap -notran -sbeg 1 -send 60 
Display a sequence with restriction cut sites, translation etc..
Input 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 shows the 'flat' format:
   

% remap -notran -sbeg 1 -send 60 -flat 
Display a sequence with restriction cut sites, translation etc..
Input 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

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -enzymes            string     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
   -sitelen            integer    Minimum recognition site length
  [-outfile]           outfile    If you enter the name of a file here then
                                  this program will write the sequence details
                                  into that file.

   Optional qualifiers:
   -mincuts            integer    Minimum cuts per RE
   -maxcuts            integer    Maximum cuts per RE
   -single             boolean    Force single site only cuts
   -[no]blunt          boolean    Allow blunt end cutters
   -[no]sticky         boolean    Allow sticky end cutters
   -[no]ambiguity      boolean    Allow ambiguous matches
   -plasmid            boolean    Allow circular DNA
   -[no]commercial     boolean    Only enzymes with suppliers
   -table              menu       Code to use
   -[no]cutlist        boolean    List the enzymes that cut
   -flatreformat       boolean    Display RE sites in flat format
   -[no]limit          boolean    Limits reports to one isoschizomer
   -preferred          boolean    Report preferred isoschizomers

   Advanced qualifiers:
   -[no]translation    boolean    Display translation
   -[no]reverse        boolean    Display cut sites and translation of reverse
                                  sense
   -orfminsize         integer    Minimum size of Open Reading Frames (ORFs)
                                  to display in the translations.
   -uppercase          range      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      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    Display protein sequences in three-letter
                                  code
   -number             boolean    Number the sequences
   -width              integer    Width of sequence to display
   -length             integer    Line length of page (0 for indefinite)
   -margin             integer    Margin around sequence for numbering
   -[no]name           boolean    Set this to be false if you do not wish to
                                  display the ID name of the sequence
   -[no]description    boolean    Set this to be false if you do not wish to
                                  display the description of the sequence
   -offset             integer    Offset to start numbering the sequence from
   -html               boolean    Use HTML formatting

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -enzymes 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 all
   -sitelen Minimum recognition site length Integer from 2 to 20 4
   [-outfile]
   (Parameter 2) If you enter the name of a file here then this program
   will write the sequence details into that file. Output file
   <sequence>.remap
   Optional qualifiers Allowed values Default
   -mincuts Minimum cuts per RE Integer from 1 to 1000 1
   -maxcuts Maximum cuts per RE Integer up to 2000000000 2000000000
   -single Force single site only cuts Boolean value Yes/No No
   -[no]blunt Allow blunt end cutters Boolean value Yes/No Yes
   -[no]sticky Allow sticky end cutters Boolean value Yes/No Yes
   -[no]ambiguity Allow ambiguous matches Boolean value Yes/No Yes
   -plasmid Allow circular DNA Boolean value Yes/No No
   -[no]commercial Only enzymes with suppliers Boolean value Yes/No Yes
   -table Code to use
   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)
   0
   -[no]cutlist List the enzymes that cut Boolean value Yes/No Yes
   -flatreformat Display RE sites in flat format Boolean value Yes/No No
   -[no]limit Limits reports to one isoschizomer Boolean value Yes/No Yes
   -preferred Report preferred isoschizomers Boolean value Yes/No No
   Advanced qualifiers Allowed values Default
   -[no]translation Display translation Boolean value Yes/No Yes
   -[no]reverse Display cut sites and translation of reverse sense
   Boolean value Yes/No Yes
   -orfminsize Minimum size of Open Reading Frames (ORFs) to display in
   the translations. Integer 0 or more 0
   -uppercase 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 Sequence range If this is left blank, then the
   sequence case is left alone.
   -highlight 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'. Sequence range full sequence
   -threeletter Display protein sequences in three-letter code Boolean
   value Yes/No No
   -number Number the sequences Boolean value Yes/No No
   -width Width of sequence to display Integer 1 or more 60
   -length Line length of page (0 for indefinite) Integer 0 or more 0
   -margin Margin around sequence for numbering Integer 0 or more 10
   -[no]name Set this to be false if you do not wish to display the ID
   name of the sequence Boolean value Yes/No Yes
   -[no]description Set this to be false if you do not wish to display
   the description of the sequence Boolean value Yes/No Yes
   -offset Offset to start numbering the sequence from Any integer value
   1
   -html Use HTML formatting Boolean value Yes/No No
   
Input file format

  Input files for usage example
  
   'tembl:eclac' is a sequence entry in the example nucleic acid database
   'tembl'
   
  Database entry: tembl:eclac
  
ID   ECLAC      standard; DNA; PRO; 7477 BP.
XX
AC   J01636; J01637; K01483; K01793;
XX
SV   J01636.1
XX
DT   30-NOV-1990 (Rel. 26, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 7)
XX
DE   E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
XX
KW   acetyltransferase; beta-D-galactosidase; galactosidase; lac operon;
KW   lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene;
KW   lacZ gene; mutagenesis; palindrome; promoter region;
KW   thiogalactoside acetyltransferase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RP   1243-1266
RX   MEDLINE; 74055539.
RA   Gilbert W., Maxam A.;
RT   "The nucleotide sequence of the lac operator";
RL   Proc. Natl. Acad. Sci. U.S.A. 70:3581-3584(1973).
XX
RN   [2]
RP   1246-1308
RX   MEDLINE; 74055540.
RA   Maizels N.M.;
RT   "The nucleotide sequence of the lactose messenger ribonucleic acid
RT   transcribed from the UV5 promoter mutant of Escherichia coli";
RL   Proc. Natl. Acad. Sci. U.S.A. 70:3585-3589(1973).
XX
RN   [3]
RX   MEDLINE; 74174501.
RA   Gilbert W., Maizels N., Maxam A.;
RT   "Sequences of controlling regions of the lactose operon";
RL   Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974).
XX
RN   [4]
RA   Gilbert W., Gralla J., Majors A.J., Maxam A.;
RT   "Lactose operator sequences and the action of lac repressor";
RL   (in) Sund H., Blauer G. (eds.);
RL   PROTEIN-LIGAND INTERACTIONS:193-207;
RL   Walter de Gruyter, New York (1975)
XX
RN   [5]
RP   1146-1282


  [Part of this file has been deleted for brevity]

     cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg      456
0
     ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg      462
0
     ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct      468
0
     ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg      474
0
     gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga      480
0
     aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct      486
0
     gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct      492
0
     ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg      498
0
     cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta      504
0
     agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg      510
0
     gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct      516
0
     ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac      522
0
     ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg      528
0
     ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct      534
0
     cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg      540
0
     tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc      546
0
     tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca      552
0
     atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg      558
0
     gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc      564
0
     gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac      570
0
     caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag      576
0
     gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt      582
0
     taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta      588
0
     aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt      594
0
     acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg      600
0
     atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg      606
0
     ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga      612
0
     taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca      618
0
     tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg      624
0
     tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact      630
0
     attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg      636
0
     ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa      642
0
     gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt      648
0
     gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc      654
0
     atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg      660
0
     atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca      666
0
     gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac      672
0
     accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc      678
0
     agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca      684
0
     ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg      690
0
     tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg      696
0
     taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc      702
0
     acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac      708
0
     caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg      714
0
     tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca      720
0
     gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca      726
0
     ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag      732
0
     cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag      738
0
     actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc      744
0
     cagcccgccc atggtaacca ccggcagagc ggtcgac                               747
7
//
   
   You can specifiy a file of ranges to display in uppercase by giving
   the '-uppercase' qualifier the value '@' followed by the name of the
   file containing the ranges. (eg: '-upper @myfile').
   
   The format of the range file is:
   
     * Comment lines start with '#' in the first column.
     * Comment lines and blank lines are ignored.
     * The line may start with white-space.
     * There are two positive (integer) numbers per line separated by one
       or more space or TAB characters.
     * The second number must be greater or equal to the first number.
     * There can be optional text after the two numbers to annotate the
       line.
     * White-space before or after the text is removed.
       
   An example range file is:

# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

   You can specifiy a file of ranges to highlight in a different colour
   when outputting in HTML format (using the '-html' qualifier) by giving
   the '-highlight' qualifier the value '@' followed by the name of the
   file containing the ranges. (eg: '-highlight @myfile').
   
   The format of this file is very similar to the format of the above
   uppercase range file, except that the text after the start and end
   positions is used as the HTML colour name. This colour name is used
   'as is' when specifying the colour in HTML in a '<FONT COLOR=xxx>'
   construct, (where 'xxx' is the name of the colour).
   
   The standard names of HTML font colours are given in:
   http://http://www.w3.org/TR/REC-html40/types.html and
   http://www.ausmall.com.au/freegraf/ncolour2.htm and
   http://mindprod.com/htmlcolours.html (amongst other places).
   
   An example highlight range file is:
     _________________________________________________________________
   
# this is my set of ranges
12   23         red
 4   5          darkturquoise
67   10348      #FFE4E1
     _________________________________________________________________
   
Output file format

  Output files for usage example
  
  File: eclac.remap
  
ECLAC
E.coli lactose operon with lacI, lacZ, lacY and lacA genes.

                                                        Bsu6I
                 TaqI                 AciI              BssKI
                 \                    \                 \
          GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                   10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
          CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                   /                    /                  / /
                   TaqI                 AciI               | BssKI
                                                           Bsu6I


# Enzymes that cut  Frequency   Isoschizomers
      AciI          1
     BssKI          1
     Bsu6I          1
      TaqI          1



# Enzymes < MINCUTS Frequency   Isoschizomers



# Enzymes > MAXCUTS Frequency   Isoschizomers



# Enzymes that do not cut




# Number of enzymes not matching SITELEN, BLUNT, STICKY, COMMERCIAL criteria

0
   
  Output files for usage example 2
  
  File: eclac.remap
  
ECLAC
E.coli lactose operon with lacI, lacZ, lacY and lacA genes.

                                                      Hin6I
                 TaqI                                 | HhaI
                 |  Bsc4I                             | Bsu6I
                 |  |   Hin6I                         | BssKI
                 |  |   | HhaI        AciI            | | BsiSI
                 \  \   \ \           \               \ \ \
          GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                   10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
          CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                 / /    / /             /             / /  ///
                 | TaqI | Hin6I         AciI          | |  ||BssKI
                 Bsc4I  HhaI                          | |  |BsiSI
                                                      | |  Bsu6I
                                                      | Hin6I
                                                      HhaI


# Enzymes that cut  Frequency   Isoschizomers
      AciI          1
     Bsc4I          1
     BsiSI          1
     BssKI          1
     Bsu6I          1
      HhaI          2
     Hin6I          2   HinP1I,HspAI
      TaqI          1



# Enzymes < MINCUTS Frequency   Isoschizomers



# Enzymes > MAXCUTS Frequency   Isoschizomers



# Enzymes that do not cut

AclI      BamHI     BceAI     Bse1I     BshI      ClaI      EcoRI     EcoRII

Hin4I     HindII    HindIII   HpyCH4IV  KpnI      NotI


# Number of enzymes not matching SITELEN, BLUNT, STICKY, COMMERCIAL criteria

0
   
  Output files for usage example 3
  
  File: eclac.remap
  
ECLAC
E.coli lactose operon with lacI, lacZ, lacY and lacA genes.

                                                                  Bsu6I
                                                        >.........====
                                                          BsiSI
                                                          >===
                        HhaI                             BssKI
                        ==>=                            >=====
                 TaqI   Hin6I                         HhaI
                 >===   >===                          ==>=
              Bsc4I                      AciI         Hin6I
              ======>====             >..====         >===
          GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                   10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
          CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
              ====<======                <===         ===<
              Bsc4I                      AciI         Hin6I
                 ===<   ===<                          =<==  <.....====
                 TaqI   Hin6I                         HhaI        Bsu6I
                        =<==                             =====<
                        HhaI                             BssKI
                                                          ===<
                                                          BsiSI


# Enzymes that cut  Frequency   Isoschizomers
      AciI          1
     Bsc4I          1
     BsiSI          1
     BssKI          1
     Bsu6I          1
      HhaI          2
     Hin6I          2   HinP1I,HspAI
      TaqI          1



# Enzymes < MINCUTS Frequency   Isoschizomers



# Enzymes > MAXCUTS Frequency   Isoschizomers



# Enzymes that do not cut

AclI      BamHI     BceAI     Bse1I     BshI      ClaI      EcoRI     EcoRII

Hin4I     HindII    HindIII   HpyCH4IV  KpnI      NotI


# Number of enzymes not matching SITELEN, BLUNT, STICKY, COMMERCIAL criteria

0
   
   The name of the sequence is displayed, followed by the description of
   the sequence.
   
   The formatted display of cut sites on the sequence follows, with the
   six-frame translation below it. The cut sites are indicated by a slash
   character '\' that points to the poition between the nucleotides where
   the cuts occur. Cuts by many enzymes at the same position are
   indicated by stacking the enzyme names on top of each other.
   
   At the end the section header 'Enzymes that cut' is displayed followed
   by a list of the enzymes that cut the specified sequence and the
   number of times that they cut. For each enzyme that cuts, a list of
   isoschizomers of that enzyme (sharing the same recognition site
   pattern and cut sites) is given.
   
   This is followed by lists of the enzymes that do cut, but which cut
   less often than the '-mincut' qualifier or more often than the
   '-maxcut' qualifier.
   
   Any of the isoschizomers that are excluded from cutting, (either
   through restrictions such as the permitted number of cuts, blunt
   cutters only, single cutters only etc. or because their name has not
   been given in the input list of enzymes), will not be listed.
   
   Then a list is displayed of the enzymes whose names were input and
   which match the other criteria ('-sitelen', '-blunt', '-sticky' or
   '-commercial') but which do not cut.
   
   Finally the number of enzymes that were rejected from consideration
   because they do not match the '-sitelen', '-blunt', '-sticky' or
   '-commercial' criteria is displayed.
   
   The '-flatreformat' qualifier changes the display to emphasise the
   recognition site of the restriction enzyme, which is indicated by a
   row of '=' characters. The cut site if pointed to by a '>' or '<'
   character and if the cut site is not within or imemdiately adjacent to
   the recognition site, they are linked by a row or '.' characters.
   
   The name of the enzyme is displayed above (or below when the reverse
   sense site if displayed) the recognition site. The name of the enzyme
   is also displayed above the cut site if this occurs on a different
   display line to the recognition site (i.e. if it wraps onto the next
   line of sequence).
   
Data files

   This uses the EMBOSS REBASE data files in 'data/REBASE/*' under the
   EMBOSS installation directory.
   
   These files must first be set up using the program 'rebaseextract'.
   Running 'rebaseextract' may be the job of your system manager.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name Description
   abiview Reads ABI file and display the trace
   backtranseq Back translate a protein sequence
   cirdna Draws circular maps of DNA constructs
   coderet Extract CDS, mRNA and translations from feature tables
   lindna Draws linear maps of DNA constructs
   pepnet Displays proteins as a helical net
   pepwheel Shows protein sequences as helices
   plotorf Plot potential open reading frames
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   recoder Remove restriction sites but maintain the same translation
   redata Search REBASE for enzyme name, references, suppliers etc
   restover Finds restriction enzymes that produce a specific overhang
   restrict Finds restriction enzyme cleavage sites
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   showfeat Show features of a sequence
   showorf Pretty output of DNA translations
   showseq Display a sequence with features, translation etc
   silent Silent mutation restriction enzyme scan
   sixpack Display a DNA sequence with 6-frame translation and ORFs
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   transeq Translate nucleic acid sequences
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Written Spring 2000
   
   Changed 7 Dec 2000 - GWW - to declare isoschizomers that cut
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
