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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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

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

## Usage

Here is a sample session with remap

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

    % remap -notran -sbeg 1 -send 60
    Display 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, (but only the prototypes of the isoschizomers are reported by default). This is run with a small test version of the restriction enzyme database and so you will probably see more enzymes when you run this.

    % remap -notran -sbeg 1 -send 60
    Display 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 is an example where all enzymes in the REBASE database are used but the -limit qualifier is not set so that all of the enzymes are displayed and not just only the prototypes of the isoschizomers. This is run with a small test version of the restriction enzyme database and so you will probably see more enzymes when you run this.

    % remap -notran -sbeg 1 -send 60 -nolimit
    Display 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 4

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

    % remap -notran -sbeg 1 -send 60 -flat
    Display 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    This sets the minimum length of the
                                      restriction enzyme recognition site. Any
                                      enzymes with sites shorter than this will be
                                      ignored.
      [-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    This sets the minimum number of cuts for any
                                      restriction enzyme that will be considered.
                                      Any enzymes that cut fewer times than this
                                      will be ignored.
       -maxcuts            integer    This sets the maximum number of cuts for any
                                      restriction enzyme that will be considered.
                                      Any enzymes that cut more times than this
                                      will be ignored.
       -single             boolean    If this is set then this forces the values
                                      of the mincuts and maxcuts qualifiers to
                                      both be 1. Any other value you may have set
                                      them to will be ignored.
       -[no]blunt          boolean    This allows those enzymes which cut at the
                                      same position on the forward and reverse
                                      strands to be considered.
       -[no]sticky         boolean    This allows those enzymes which cut at
                                      different positions on the forward and
                                      reverse strands, leaving an overhang, to be
                                      considered.
       -[no]ambiguity      boolean    This allows those enzymes which have one or
                                      more 'N' ambiguity codes in their pattern to
                                      be considered
       -plasmid            boolean    If this is set then this allows searches for
                                      restriction enzyme recognition site and cut
                                      postions that span the end of the sequence
                                      to be considered.
       -[no]commercial     boolean    If this is set, then only those enzymes with
                                      a commercial supplier will be searched for.
                                      This qualifier is ignored if you have
                                      specified an explicit list of enzymes to
                                      search for, rather than searching through
                                      'all' the enzymes in the REBASE database. It
                                      is assumed that, if you are asking for an
                                      explicit enzyme, then you probably know
                                      where to get it from and so all enzymes
                                      names that you have asked to be searched
                                      for, and which cut, will be reported whether
                                      or not they have a commercial supplier.
       -table              menu       Genetic code to use
       -[no]cutlist        boolean    This produces lists in the output of the
                                      enzymes that cut, those that cut but are
                                      excluded because that cut fewer times than
                                      mincut or more times than maxcut and those
                                      enzymes that do not cut.
       -flatreformat       boolean    This changes the output format to one where
                                      the recognition site is indicated by a row
                                      of '===' characters and the cut site is
                                      pointed to by a '>' character in the forward
                                      sense, or a '<' in the reverse sense
                                      strand.
       -[no]limit          boolean    This limits the reporting of enzymes to just
                                      one enzyme from each group of
                                      isoschizomers. The enzyme chosen to
                                      represent an isoschizomer group is the
                                      prototype indicated in the data file
                                      'embossre.equ', which is created by the
                                      program 'rebaseextract'. If you prefer
                                      different prototypes to be used, make a copy
                                      of embossre.equ in your home directory and
                                      edit it. If this value is set to be false
                                      then all of the input enzymes will be
                                      reported. You might like to set this to
                                      false if you are supplying an explicit set
                                      of enzymes rather than searching 'all' of
                                      them.

       Advanced qualifiers:
       -[no]translation    boolean    This displays the 6-frame translations of
                                      the sequence in the output.
       -[no]reverse        boolean    This displays the cut sites and translation
                                      of the reverse sense.
       -orfminsize         integer    This sets the minimum size of Open Reading
                                      Frames (ORFs) to display in the
                                      translations. All other translation regions
                                      are masked by changing the amino acids to
                                      '-' characters.
       -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

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related qualifiers
       -odirectory2         string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

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 | This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. | Integer from 2 to 20 | 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 | This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored. | Integer from 1 to 1000 | 1
-maxcuts | This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored. | Integer up to 2000000000 | 2000000000
-single | If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored. | Boolean value Yes/No | No
-[no]blunt | This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. | Boolean value Yes/No | Yes
-[no]sticky | This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. | Boolean value Yes/No | Yes
-[no]ambiguity | This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered | Boolean value Yes/No | Yes
-plasmid | If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered. | Boolean value Yes/No | No
-[no]commercial | If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier. | Boolean value Yes/No | Yes
-table | Genetic 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 | This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut. | Boolean value Yes/No | Yes
-flatreformat | This changes the output format to one where the recognition site is indicated by a row of '===' characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the reverse sense strand. | Boolean value Yes/No | No
-[no]limit | This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them. | Boolean value Yes/No | Yes
Advanced qualifiers | Allowed values | Default
-[no]translation | This displays the 6-frame translations of the sequence in the output. | Boolean value Yes/No | Yes
-[no]reverse | This displays the cut sites and translation of the reverse sense. | Boolean value Yes/No | Yes
-orfminsize | This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to '-' characters. | Integer 0 or more | If this value is left as 0 then all of the translation is shown.
-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      4560
         ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg      4620
         ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct      4680
         ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg      4740
         gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga      4800
         aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct      4860
         gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct      4920
         ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg      4980
         cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta      5040
         agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg      5100
         gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct      5160
         ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac      5220
         ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg      5280
         ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct      5340
         cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg      5400
         tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc      5460
         tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca      5520
         atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg      5580
         gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc      5640
         gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac      5700
         caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag      5760
         gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt      5820
         taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta      5880
         aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt      5940
         acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg      6000
         atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg      6060
         ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga      6120
         taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca      6180
         tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg      6240
         tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact      6300
         attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg      6360
         ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa      6420
         gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt      6480
         gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc      6540
         atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg      6600
         atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca      6660
         gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac      6720
         accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc      6780
         agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca      6840
         ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg      6900
         tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg      6960
         taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc      7020
         acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac      7080
         caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg      7140
         tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca      7200
         gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca      7260
         ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag      7320
         cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag      7380
         actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc      7440
         cagcccgccc atggtaacca ccggcagagc ggtcgac                               7477
    //

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.

                                                            BssKI
                     TaqI                 AciI              Ksp632I
                     \                    \                 \
              GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                       /                    /                  / /
                       TaqI                 AciI               | BssKI
                                                               Ksp632I

    # Enzymes that cut  Frequency	Isoschizomers
          AciI	    1
         BssKI	    1
       Ksp632I	    1	Bsu6I
          TaqI	    1

    # Enzymes < MINCUTS Frequency	Isoschizomers

    # Enzymes > MAXCUTS Frequency	Isoschizomers

    # Enzymes that do not cut

    # No. of cutting REs 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
                     |  BsiYI                             | BssKI
                     |  |   Hin6I                         | Ksp632I
                     |  |   | HhaI        AciI            | | HpaII
                     \  \   \ \           \               \ \ \
              GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                     / /    / /             /             / /  ///
                     | TaqI | Hin6I         AciI          | |  ||BssKI
                     BsiYI  HhaI                          | |  |HpaII
                                                          | |  Ksp632I
                                                          | Hin6I
                                                          HhaI

    # Enzymes that cut  Frequency	Isoschizomers
          AciI	    1
         BsiYI	    1	Bsc4I
         BssKI	    1
          HhaI	    2
         Hin6I	    2	HinP1I,HspAI
         HpaII	    1	BsiSI
       Ksp632I	    1	Bsu6I
          TaqI	    1

    # Enzymes < MINCUTS Frequency	Isoschizomers

    # Enzymes > MAXCUTS Frequency	Isoschizomers

    # Enzymes that do not cut

    AclI      BamHI     BceAI     BsrI      ClaI      EcoRI     EcoRII    HaeIII
    Hin4I     HindII    HindIII   KpnI      MaeII     NotI

    # No. of cutting REs 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.

                                                          HspAI
                     TaqI                                 Hin6I
                     |  Bsc4I                             HinP1I
                     |  |   HspAI                         | HhaI
                     |  |   Hin6I                         | BssKI
                     |  |   HinP1I                        | Bsu6I
                     |  |   | HhaI        AciI            | | BsiSI
                     \  \   \ \           \               \ \ \
              GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                     / /    / /             /             / /  ///
                     | TaqI | HinP1I        AciI          | |  ||BssKI
                     Bsc4I  | Hin6I                       | |  |BsiSI
                            | HspAI                       | |  Bsu6I
                            HhaI                          | HinP1I
                                                          | HspAI
                                                          | Hin6I
                                                          HhaI

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

    # Enzymes < MINCUTS Frequency

    # Enzymes > MAXCUTS Frequency

    # Enzymes that do not cut

    AclI      BamHI     BceAI     Bse1I     BshI      ClaI      EcoRI     EcoRII
    Hin4I     HindII    HindIII   HpyCH4IV  KpnI      NotI

    # No. of cutting REs not matching SITELEN, BLUNT, STICKY, COMMERCIAL criteria

    0

### Output files for usage example 4

### File: eclac.remap

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

                                                                      Ksp632I
                                                            >.........====
                                                              HpaII
                                                              >===
                            HhaI                             BssKI
                            ==>=                            >=====
                     TaqI   Hin6I                         HhaI
                     >===   >===                          ==>=
                  BsiYI                      AciI         Hin6I
                  ======>====             >..====         >===
              GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGT
                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              CTGTGGTAGCTTACCGCGTTTTGGAAAGCGCCATACCGTACTATCGCGGGCCTTCTCTCA
                  ====<======                <===         ===<
                  BsiYI                      AciI         Hin6I
                     ===<   ===<                          =<==  <.....====
                     TaqI   Hin6I                         HhaI        Ksp632I
                            =<==                             =====<
                            HhaI                             BssKI
                                                              ===<
                                                              HpaII

    # Enzymes that cut  Frequency	Isoschizomers
          AciI	    1
         BsiYI	    1	Bsc4I
         BssKI	    1
          HhaI	    2
         Hin6I	    2	HinP1I,HspAI
         HpaII	    1	BsiSI
       Ksp632I	    1	Bsu6I
          TaqI	    1

    # Enzymes < MINCUTS Frequency	Isoschizomers

    # Enzymes > MAXCUTS Frequency	Isoschizomers

    # Enzymes that do not cut

    AclI      BamHI     BceAI     BsrI      ClaI      EcoRI     EcoRII    HaeIII
    Hin4I     HindII    HindIII   KpnI      MaeII     NotI

    # No. of cutting REs 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.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

The data files are stored in the REBASE directory of the standard EMBOSS data directory. The names are:

- embossre.enz Cleavage information
- embossre.ref Reference/methylation information
- embossre.sup Supplier information

The column information is described at the top of the data files

The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype,if you wish.

The format of the file "embossre.equ" is
Enzyme-name Prototype-name

i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred, prototype name.

## 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)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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