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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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/rebase/rebase.html

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
  [-outfile]           outfile    If you enter the name of a file here then
                                  this program will write the sequence details
                                  into that file.
   -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

   Optional qualifiers:
   -[no]cutlist        bool       List the enzymes that cut
   -flatreformat       bool       Display RE sites in flat format
   -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
   -[no]limit          bool       Limits reports to one isoschizomer
   -preferred          bool       Report preferred isoschizomers
   -table              list       Code to use

   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
[-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
-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
Optional qualifiers Allowed values Default
-[no]cutlist List the enzymes that cut Yes/No Yes
-flatreformat Display RE sites in flat format Yes/No No
-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
-[no]limit Limits reports to one isoschizomer Yes/No Yes
-preferred Report preferred isoschizomers Yes/No No
-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
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:

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://www.iconbazaar.com/color_tables/named_colors.html

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	PflMI,Van91I
     AccII	    1	Bsh1236I,BstFNI,BstUI,MvnI,ThaI
      AciI	    1	
    AspLEI	    2	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 that do not cut

AatI      AatII     AauI      Acc113I   Acc16I    Acc36I    Acc65I    AccB1I    
AccBSI    AccI      AccIII    AclI      AclNI     AclWI     AcsI      AcyI      
AdeI      AfaI      AfeI      AflII     AflIII    AgeI      AhdI      AloI      
AluI      Alw21I    Alw26I    Alw44I    AlwI      AlwNI     Ama87I    AocI      
Aor51HI   ApaI      ApaLI     ApoI      AscI      AseI      AsiAI     AsnI      
Asp700I   Asp718I   AspEI     AspHI     AspI      AspS9I    AsuHPI    AsuNHI    
AvaI      AvaII     AviII     AvrII     AxyI      BaeI      BalI      BamHI     
BanI      BanII     BanIII    BbeI      BbrPI     BbsI      BbuI      Bbv12I    
BbvCI     BbvI      BcgI      BciVI     BclI      BcoI      BcuI      BfaI      
BfmI      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     BseCI     BseDI     
BseGI     BseMI     BseMII    BseNI     BsePI     BseRI     BseSI     BseX3I    
BseXI     BsgI      Bsh1285I  Bsh1365I  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     BspDI     BspEI     BspHI     BspLI     
BspLU11I  BspMI     BspPI     BspTI     BspXI     BsrBI     BsrBRI    BsrDI     
BsrFI     BsrGI     BsrI      BsrSI     BssAI     BssECI    BssHII    BssNAI    
BssSI     BssT1I    Bst1107I  Bst2BI    Bst2UI    Bst4CI    Bst71I    Bst98I    
BstACI    BstAPI    BstBAI    BstBI     BstDEI    BstDSI    BstEII    BstF5I    
BstHPI    BstMCI    BstNI     BstNSI    BstOI     BstPAI    BstPI     BstSFI    
BstSNI    BstX2I    BstXI     BstYI     BstZ17I   BstZI     Bsu15I    Bsu36I    
BsuRI     BtgI      BtrI      BtsI      Cac8I     CaiI      CciNI     CelII     
Cfr10I    Cfr13I    Cfr42I    Cfr9I     CfrI      ClaI      CpoI      Csp45I    
Csp6I     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    
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    FspI      GsuI      HaeIII    HgaI      
HgiEI     Hin1I     HincII    HindII    HindIII   HinfI     HpaI      HphI      
Hpy188I   Hpy188III Hpy8I     Hpy99I    HpyCH4III HpyCH4IV  HpyCH4V   Hsp92I    
ItaI      KasI      Kpn2I     KpnI      Ksp22I    KspAI     KspI      Kzo9I     
LspI      MaeI      MaeII     MaeIII    MamI      MbiI      MboI      MboII     
MfeI      MflI      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      NspBII    NspI      
NspV      PacI      PaeI      PaeR7I    PagI      PalI      PauI      PciI      
PdiI      PdmI      Pfl23II   PflFI     PinAI     Ple19I    PleI      PmaCI     
Pme55I    PmeI      PmlI      PpiI      PpsI      Ppu10I    PpuMI     PshAI     
PshBI     PsiI      Psp124BI  Psp1406I  Psp5II    PspAI     PspEI     PspGI     
PspLI     PspN4I    PspOMI    PspPPI    PstI      PsuI      PsyI      PvuI      
PvuII     RcaI      RsaI      Rsr2I     RsrII     SacI      SacII     SalI      
SanDI     SapI      Sau3AI    Sau96I    SbfI      ScaI      SchI      SdaI      
SduI      SexAI     SfaNI     SfcI      SfiI      SfoI      Sfr274I   Sfr303I   
SfuI      SgfI      SgrAI     SinI      SmaI      SmiI      SmiMI     SmlI      
SnaBI     SpeI      SphI      SrfI      Sse8387I  Sse9I     SseBI     SspBI     
SspI      SstI      SstII     StuI      StyI      SunI      SwaI      TaaI      
TaiI      TasI      TatI      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      
Zsp2I

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.

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.

Finally, a list of the enzymes whose names were input but which do not cut is given.

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..

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 that do not cut


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 nameDescription
abiviewReads ABI file and display the trace
backtranseqBack translate a protein sequence
cirdnaDraws circular maps of DNA constructs
coderetExtract CDS, mRNA and translations from feature tables
lindnaDraws linear maps of DNA constructs
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
plotorfPlot potential open reading frames
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
recoderRemove restriction sites but maintain the same translation
redataSearch REBASE for enzyme name, references, suppliers etc
restoverFinds restriction enzymes that produce a specific overhang
restrictFinds restriction enzyme cleavage sites
seealsoFinds programs sharing group names
showalignDisplay a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showorfPretty output of DNA translations
showseqDisplay a sequence with features, translation etc
silentSilent mutation restriction enzyme scan
textsearchSearch sequence documentation text. SRS and Entrez are faster!
transeqTranslate 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