
                               EMBOSS: remap
     _________________________________________________________________
   
                                 Program 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   contains published and unpublished references, recognition and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. We only look at a small section
   of the sequence to save space.
% remap -notran -sbeg 1 -send 60
Display a sequence with restriction cut sites, translation etc..
Input sequence(s): embl:eclac
Output file [eclac.remap]:
Comma separated enzyme list [all]: taqi,bsu6i,acii,bsski
Minimum recognition site length [4]:

   Here 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): embl:eclac
Output file [eclac.remap]:
Comma separated enzyme list [all]:
Minimum recognition site length [4]:

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

   Advanced qualifiers:
   -[no]translation    bool       Display translation
   -[no]reverse        bool       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        bool       Display protein sequences in three-letter
                                  code
   -number             bool       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           bool       Set this to be false if you do not wish to
                                  display the ID name of the sequence
   -[no]description    bool       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               bool       Use HTML formatting

   General qualifiers:
  -help                bool       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 Yes/No No
   -[no]blunt Allow blunt end cutters Yes/No Yes
   -[no]sticky Allow sticky end cutters Yes/No Yes
   -[no]ambiguity Allow ambiguous matches Yes/No Yes
   -plasmid Allow circular DNA Yes/No No
   -[no]commercial Only enzymes with suppliers 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 Yes/No Yes
   -flatreformat Display RE sites in flat format Yes/No No
   -[no]limit Limits reports to one isoschizomer Yes/No Yes
   -preferred Report preferred isoschizomers Yes/No No
   Advanced qualifiers Allowed values Default
   -[no]translation Display translation Yes/No Yes
   -[no]reverse Display cut sites and translation of reverse sense 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 Yes/No No
   -number Number the sequences 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 Yes/No Yes
   -[no]description Set this to be false if you do not wish to display
   the description of the sequence Yes/No Yes
   -offset Offset to start numbering the sequence from Any integer value
   1
   -html Use HTML formatting Yes/No No
   
Input file format

   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

   The output file from the example above, where all enzymes were used,
   follows:
     _________________________________________________________________
   
ECLAC
E.coli lactose operon with lacI, lacZ, lacY and lacA genes.

                                                  Hsp92II
                                                  |   Hin6I
                                                  |   | Bsu6I
                                                  |   | BssKI
                 TaqI                             |   | AspLEI
                 |  Bsc4I                         |   | |Bsp143II
                 |  AccB7I                        |   | ||BsiSI
                 |  |   Hin6I         AciI        |   | ||AsuC2I
                 |  |   | AspLEI      AccII       |   | ||Bme1390I
                 \  \   \ \           \           \   \ \\\
          GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                   10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
          CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                 / /    / /           / /     /      // /  ///
                 | TaqI | Hin6I       | AciI  |      || |  ||BssKI
                 AccB7I AspLEI        AccII   |      || |  |BsiSI
                 Bsc4I                        |      || |  Bme1390I
                                              |      || |  AsuC2I
                                              |      || |  Bsu6I
                                              |      || Hin6I
                                              |      |AspLEI
                                              |      Bsp143II
                                              Hsp92II


# Enzymes that cut  Frequency   Isoschizomers
    AccB7I          1   PflBI,PflMI,Van91I
     AccII          1   Bsh1236I,BstFNI,BstUI,MvnI,ThaI
      AciI          1
    AspLEI          2   BstHHI,CfoI,HhaI
    AsuC2I          1   BcnI,NciI
  Bme1390I          1   MspR9I,ScrFI
     Bsc4I          1   BseLI,BsiYI,BslI
     BsiSI          1   HapII,HpaII,MspI
  Bsp143II          1   BstH2I,HaeII
     BssKI          1
     Bsu6I          1   Eam1104I,EarI,Ksp632I
     Hin6I          2   HinP1I,HspAI
   Hsp92II          1   NlaIII
      TaqI          1   TthHB8I



# Enzymes < MINCUTS Frequency   Isoschizomers



# Enzymes > MAXCUTS Frequency   Isoschizomers



# Enzymes that do not cut

AarI      AatI      AatII     AauI      Acc113I   Acc16I    Acc36I    Acc65I

AccB1I    AccBSI    AccI      AccIII    AclI      AclWI     AcsI      AcyI

AdeI      AfaI      AfeI      AflI      AflII     AflIII    AgeI      AhdI

AhlI      AloI      AluI      Alw21I    Alw26I    Alw44I    AlwI      AlwNI

Ama87I    AocI      Aor51HI   ApaI      ApaLI     ApoI      AscI      AseI

AsiAI     AsnI      Asp700I   Asp718I   AspEI     AspHI     AspI      AspS9I

AsuHPI    AsuII     AsuNHI    AvaI      AvaII     AviII     AvrII     AxyI

BaeI      BalI      BamHI     BanI      BanII     BanIII    BbeI      BbrPI

BbsI      BbuI      Bbv12I    BbvCI     BbvI      BceAI     BcgI      BciVI

BclI      BcoI      BcuI      BfaI      BfiI      BfmI      BfrBI     BfrI

BfuI      BglI      BglII     BlnI      BlpI      Bme18I    BmrI      BmyI

BoxI      BpiI      BplI      BpmI      Bpu10I    Bpu1102I  Bpu14I    BpuAI

Bsa29I    BsaAI     BsaBI     BsaHI     BsaI      BsaJI     BsaMI     BsaOI

BsaWI     BsaXI     BscBI     BscCI     BscFI     BscI      Bse118I   Bse1I

Bse21I    Bse3DI    Bse8I     BseAI     BseBI     BseCI     BseDI     BseGI

BseMI     BseMII    BseNI     BsePI     BseRI     BseSI     BseX3I    BseXI

BsgI      Bsh1285I  Bsh1365I  BshFI     BshI      BshNI     BshTI     BsiBI

BsiCI     BsiEI     BsiHKAI   BsiLI     BsiMI     BsiQI     BsiWI     BsiXI

BsiZI     BsmAI     BsmBI     BsmFI     BsmI      Bso31I    BsoBI     BsoMAI

Bsp106I   Bsp119I   Bsp120I   Bsp1286I  Bsp13I    Bsp1407I  Bsp143I   Bsp1720I

Bsp19I    Bsp68I    BspA2I    BspCI     BspCNI    BspDI     BspEI     BspHI

BspLI     BspLU11I  BspMI     BspPI     BspT104I  BspT107I  BspTI     BspXI

BsrBI     BsrBRI    BsrDI     BsrFI     BsrGI     BsrI      BsrSI     BssAI

BssECI    BssHI     BssHII    BssNAI    BssSI     BssT1I    Bst1107I  Bst2BI

Bst2UI    Bst4CI    Bst71I    Bst98I    BstACI    BstAPI    BstBAI    BstBI

BstDEI    BstDSI    BstEII    BstENI    BstENII   BstF5I    BstHPI    BstMCI

BstNI     BstNSI    BstOI     BstPAI    BstPI     BstSFI    BstSNI    BstV2I

BstX2I    BstXI     BstYI     BstZ17I   BstZI     Bsu15I    Bsu36I    BsuRI

BtgI      BtrI      BtsI      Cac8I     CaiI      CciNI     CelII     Cfr10I

Cfr13I    Cfr42I    Cfr9I     CfrI      ClaI      CpoI      Csp45I    Csp6I

CspAI     CspI      CviJI     CviRI     CviTI     CvnI      DdeI      DpnI

DpnII     DraI      DraII     DraIII    DrdI      DsaI      DseDI     EaeI

EagI      Eam1105I  EciI      Ecl136II  EclHKI    EclXI     Eco105I   Eco130I

Eco147I   Eco24I    Eco31I    Eco32I    Eco47I    Eco47III  Eco52I    Eco57I

Eco57MI   Eco64I    Eco72I    Eco81I    Eco88I    Eco91I    EcoICRI   EcoNI

EcoO109I  EcoO65I   EcoRI     EcoRII    EcoRV     EcoT14I   EcoT22I   EcoT38I

EgeI      EheI      ErhI      Esp3I     FauI      FauNDI    FbaI      FblI

Fnu4HI    FokI      FriOI     FseI      Fsp4HI    FspAI     FspI      FunI

FunII     GsuI      HaeIII    HgaI      HgiEI     Hin1I     Hin4I     HincII

HindII    HindIII   HinfI     HpaI      HphI      Hpy188I   Hpy188III Hpy8I

Hpy99I    HpyCH4III HpyCH4IV  HpyCH4V   HpyF44III Hsp92I    ItaI      KasI

Kpn2I     KpnI      Ksp22I    KspAI     KspI      Kzo9I     LspI      LweI

MabI      MaeI      MaeII     MaeIII    MamI      MbiI      MboI      MboII

MfeI      MflI      MhlI      MlsI      MluI      MluNI     Mly113I   MlyI

MnlI      Mph1103I  MroI      MroNI     MroXI     MscI      MseI      MslI

Msp17I    MspA1I    MspCI     MssI      MunI      Mva1269I  MvaI      MwoI

NaeI      NarI      NcoI      NdeI      NdeII     NgoAIV    NgoMIV    NheI

NlaIV     NmuCI     NotI      NruGI     NruI      NsbI      NsiI      NspI

NspIII    NspV      OliI      PacI      PaeI      PaeR7I    PagI      PalI

PauI      PciI      PctI      PdiI      PdmI      Pfl23II   PflFI     PinAI

Ple19I    PleI      PmaCI     Pme55I    PmeI      PmlI      PpiI      PpsI

Ppu10I    PpuMI     PpuXI     PshAI     PshBI     PsiI      Psp124BI  Psp1406I

Psp5II    PspAI     PspEI     PspGI     PspLI     PspN4I    PspOMI    PspPI

PspPPI    PsrI      PstI      PsuI      PsyI      PvuI      PvuII     RcaI

RsaI      Rsr2I     RsrII     SacI      SacII     SalI      SanDI     SapI

SatI      Sau3AI    Sau96I    SbfI      ScaI      SchI      SdaI      SduI

SexAI     SfaNI     SfcI      SfiI      SfoI      Sfr274I   Sfr303I   SfuI

SgfI      SgrAI     SgrBI     SinI      SlaI      SmaI      SmiI      SmiMI

SmlI      SmuI      SnaBI     SpaHI     SpeI      SphI      SrfI      Sse8387I

Sse9I     SseBI     SspBI     SspI      SstI      SstII     StuI      StyI

SunI      SwaI      TaaI      TaiI      TasI      TatI      TauI      TelI

TfiI      TliI      Tru1I     Tru9I     TscI      TseI      Tsp45I    Tsp509I

TspEI     TspRI     Tth111I   Vha464I   VneI      VpaK11BI  VspI      XagI

XapI      XbaI      XceI      XcmI      XhoI      XhoII     XmaCI     XmaI

XmaIII    XmaJI     XmiI      XmnI      XspI      ZhoI      Zsp2I


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

633
     _________________________________________________________________
   
   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).
   
   An example of this display follows with the translation turned off to
   save space:

% remap embl:eclac stdout -enz taqi,bsu6i,acii,hin6i,bsski -site 4
-sbeg 1 -send 60 -flat -notran
Display a sequence with restriction cut sites, translation etc..

ECLAC
E.coli lactose operon with lacI, lacZ, lacY and lacA genes.

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


# Enzymes that cut  Frequency   Isoschizomers
      AciI          1
     BssKI          1
     Bsu6I          1
     Hin6I          2
      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

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
   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
