EMBOSS: remap

| ## 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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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