| restrict

## Function

Finds restriction enzyme cleavage sites

## Description

Restrict uses the REBASE database of restriction enzymes to predict cut sites in a DNA sequence. The program allows you to select a range of cuts, whether the DNA is circular, whether IUB ambiguity codes are used, whether blunt or sticky ends or both are reported. You may also force the reporting of single cleavage sites.

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 restrict

    % restrict
    Finds restriction enzyme cleavage sites
    Input sequence(s): tembl:hsfau
    Minimum recognition site length [4]:
    Comma separated enzyme list [all]:
    Output report [hsfau.restrict]:

Go to the input files for this example
Go to the output files for this example

Example 2

This gives the lengths of the restriction fragments produced by cutting with all of the specified enzymes.

    % restrict -fragments
    Finds restriction enzyme cleavage sites
    Input sequence(s): tembl:hsfau
    Minimum recognition site length [4]:
    Comma separated enzyme list [all]:
    Output report [hsfau.restrict]:

Go to the output files for this example

Example 3

This gives the lengths of the restriction fragments created by cutting with just one of each of the specified enzymes in turn.

    % restrict -solofragment
    Finds restriction enzyme cleavage sites
    Input sequence(s): tembl:hsfau
    Minimum recognition site length [4]:
    Comma separated enzyme list [all]:
    Output report [hsfau.restrict]:

Go to the output files for this example

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -sitelen            integer    This sets the minimum length of the
                                      restriction enzyme recognition site. Any
                                      enzymes with sites shorter than this will be
                                      ignored.
       -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
      [-outfile]           report     Output report file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -min                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.
       -max                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.
       -solofragment       boolean    This gives the fragment lengths of the
                                      forward sense strand produced by complete
                                      restriction by each restriction enzyme on it
                                      own. Results are added to the tail section
                                      of the report.
       -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.
       -datafile           string     Alternative RE data file
       -[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.
       -alphabetic         boolean    Sort output alphabetically
       -fragments          boolean    This gives the fragment lengths of the
                                      forward sense strand produced by complete
                                      restriction using all of the input enzymes
                                      together. Results are added to the tail
                                      section of the report.
       -name               boolean    Show sequence name

       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
       -rformat2            string     Report format
       -rname2              string     Base file name
       -rextension2         string     File name extension
       -rdirectory2         string     Output directory
       -raccshow2           boolean    Show accession number in the report
       -rdesshow2           boolean    Show description in the report
       -rscoreshow2         boolean    Show the score in the report
       -rusashow2           boolean    Show the full USA in the report

       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
-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
-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
[-outfile] (Parameter 2) | Output report file name | Report output file |
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-min | 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
-max | 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
-solofragment | This gives the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on it own. Results are added to the tail section of the report. | Boolean value Yes/No | No
-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
-datafile | Alternative RE data file | Any string is accepted | An empty string is accepted
-[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
-alphabetic | Sort output alphabetically | Boolean value Yes/No | No
-fragments | This gives the fragment lengths of the forward sense strand produced by complete restriction using all of the input enzymes together. Results are added to the tail section of the report. | Boolean value Yes/No | No
-name | Show sequence name | Boolean value Yes/No | No

## Input file format

restrict reads one or more DNA sequence USAs.

### Input files for usage example

'tembl:hsfau' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:hsfau

    ID   HSFAU      standard; RNA; HUM; 518 BP.
    XX
    AC   X65923;
    XX
    SV   X65923.1
    XX
    DT   13-MAY-1992 (Rel. 31, Created)
    DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
    XX
    DE   H.sapiens fau mRNA
    XX
    KW   fau gene.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-518
    RA   Michiels L.M.R.;
    RT   ;
    RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
    RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
    RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
    XX
    RN   [2]
    RP   1-518
    RX   MEDLINE; 93368957.
    RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
    RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
    RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
    RL   Oncogene 8:2537-2546(1993).
    XX
    DR   SWISS-PROT; P35544; UBIM_HUMAN.
    DR   SWISS-PROT; Q05472; RS30_HUMAN.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..518
    FT                   /chromosome="11q"
    FT                   /db_xref="taxon:9606"
    FT                   /organism="Homo sapiens"
    FT                   /tissue_type="placenta"
    FT                   /clone_lib="cDNA"
    FT                   /clone="pUIA 631"
    FT                   /map="13"
    FT   misc_feature    57..278
    FT                   /note="ubiquitin like part"
    FT   CDS             57..458
    FT                   /db_xref="SWISS-PROT:P35544"
    FT                   /db_xref="SWISS-PROT:Q05472"
    FT                   /gene="fau"
    FT                   /protein_id="CAA46716.1"
    FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
    FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
    FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
    FT   misc_feature    98..102
    FT                   /note="nucleolar localization signal"
    FT   misc_feature    279..458
    FT                   /note="S30 part"
    FT   polyA_signal    484..489
    FT   polyA_site      509
    XX
    SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
         ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
         agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
         cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
         tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
         tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
         gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
         agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
         cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
         tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
    //

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default restrict writes a 'table' report file.

### Output files for usage example

### File: hsfau.restrict

    ########################################
    # Program: restrict
    # Rundate: Thu May 22 13:31:43 2003
    # Report_format: table
    # Report_file: hsfau.restrict
    ########################################

    #=======================================
    #
    # Sequence: HSFAU     from: 1   to: 518
    # HitCount: 53
    #
    # Minimum cuts per enzyme: 1
    # Maximum cuts per enzyme: 2000000000
    # Minimum length of recognition site: 4
    # Blunt ends allowed
    # Sticky ends allowed
    # DNA is linear
    # Ambiguities allowed
    #
    #=======================================

      Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
         11      14 TaqI        TCGA                 11     13         .         .
         28      31 AciI        CCGC                 25     27         .         .
         38      41 AciI        CCGC                 38     40         .         .
         44      48 BceAI       ACGGC                25     27         .         .
         71      74 AciI        CCGC                 71     73         .         .
         71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
         73      76 Hin6I       GCGC                 73     75         .         .
         73      76 HhaI        GCGC                 75     73         .         .
         77      81 BssKI       CCNGG                76     81         .         .
         77      81 EcoRII      CCWGG                76     81         .         .
         94      97 TaqI        TCGA                 94     96         .         .
        103     106 HpaII       CCGG                103    105         .         .
        105     108 HaeIII      GGCC                106    106         .         .
        107     111 EcoRII      CCWGG               106    111         .         .
        107     117 BsiYI       CCNNNNNNNGG         113    110         .         .
        107     111 BssKI       CCNGG               106    111         .         .
        122     132 BsiYI       CCNNNNNNNGG         128    125         .         .
        125     135 Hin4I       GAYNNNNNVTC         116    111       148       143
        146     150 BsrI        ACTGG               151    149         .         .
        161     165 BssKI       CCNGG               160    165         .         .
        162     165 HpaII       CCGG                162    164         .         .
        182     186 BssKI       CCNGG               181    186         .         .
        182     186 EcoRII      CCWGG               181    186         .         .
        190     193 HhaI        GCGC                192    190         .         .
        190     193 Hin6I       GCGC                190    192         .         .
        192     195 HhaI        GCGC                194    192         .         .
        192     195 Hin6I       GCGC                192    194         .         .
        197     201 BssKI       CCNGG               196    201         .         .
        197     201 EcoRII      CCWGG               196    201         .         .
        209     212 HaeIII      GGCC                210    210         .         .
        219     222 HaeIII      GGCC                220    220         .         .
        221     231 BsiYI       CCNNNNNNNGG         227    224         .         .
        225     229 BsrI        ACTGG               221    219         .         .
        229     232 AciI        CCGC                226    228         .         .
        236     239 HaeIII      GGCC                237    237         .         .
        248     252 BssKI       CCNGG               247    252         .         .
        248     252 EcoRII      CCWGG               247    252         .         .
        261     264 HaeIII      GGCC                262    262         .         .
        263     266 AciI        CCGC                263    265         .         .
        293     297 EcoRII      CCWGG               292    297         .         .
        293     297 BssKI       CCNGG               292    297         .         .
        296     299 HaeIII      GGCC                297    297         .         .
        335     338 HaeIII      GGCC                336    336         .         .
        380     383 AciI        CCGC                377    379         .         .
        383     386 AciI        CCGC                380    382         .         .
        395     398 HpaII       CCGG                395    397         .         .
        398     401 HhaI        GCGC                400    398         .         .
        398     401 Hin6I       GCGC                398    400         .         .
        405     410 HindII      GTYRAC              407    407         .         .
        408     413 AclI        AACGTT              409    411         .         .
        409     412 MaeII       ACGT                409    411         .         .
        417     427 BsiYI       CCNNNNNNNGG         423    420         .         .
        438     441 HaeIII      GGCC                439    439         .         .

    #---------------------------------------
    #---------------------------------------

### Output files for usage example 2

### File: hsfau.restrict

    ########################################
    # Program: restrict
    # Rundate: Thu May 22 15:01:50 2003
    # Report_format: table
    # Report_file: hsfau.restrict
    ########################################

    #=======================================
    #
    # Sequence: HSFAU     from: 1   to: 518
    # HitCount: 53
    #
    # Minimum cuts per enzyme: 1
    # Maximum cuts per enzyme: 2000000000
    # Minimum length of recognition site: 4
    # Blunt ends allowed
    # Sticky ends allowed
    # DNA is linear
    # Ambiguities allowed
    #
    #=======================================

      Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
         11      14 TaqI        TCGA                 11     13         .         .
         28      31 AciI        CCGC                 25     27         .         .
         38      41 AciI        CCGC                 38     40         .         .
         44      48 BceAI       ACGGC                25     27         .         .
         71      74 AciI        CCGC                 71     73         .         .
         71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
         73      76 Hin6I       GCGC                 73     75         .         .
         73      76 HhaI        GCGC                 75     73         .         .
         77      81 BssKI       CCNGG                76     81         .         .
         77      81 EcoRII      CCWGG                76     81         .         .
         94      97 TaqI        TCGA                 94     96         .         .
        103     106 HpaII       CCGG                103    105         .         .
        105     108 HaeIII      GGCC                106    106         .         .
        107     111 EcoRII      CCWGG               106    111         .         .
        107     117 BsiYI       CCNNNNNNNGG         113    110         .         .
        107     111 BssKI       CCNGG               106    111         .         .
        122     132 BsiYI       CCNNNNNNNGG         128    125         .         .
        125     135 Hin4I       GAYNNNNNVTC         116    111       148       143
        146     150 BsrI        ACTGG               151    149         .         .
        161     165 BssKI       CCNGG               160    165         .         .
        162     165 HpaII       CCGG                162    164         .         .
        182     186 BssKI       CCNGG               181    186         .         .
        182     186 EcoRII      CCWGG               181    186         .         .
        190     193 HhaI        GCGC                192    190         .         .
        190     193 Hin6I       GCGC                190    192         .         .
        192     195 HhaI        GCGC                194    192         .         .
        192     195 Hin6I       GCGC                192    194         .         .

      [Part of this file has been deleted for brevity]

    #---------------------------------------
    #
    # Fragment lengths:
    #     79
    #     41
    #     39
    #     33
    #     29
    #     20
    #     19
    #     17
    #     16
    #     15
    #     15
    #     14
    #     14
    #     14
    #     13
    #     12
    #     11
    #     10
    #     10
    #     10
    #     9
    #     9
    #     9
    #     7
    #     7
    #     5
    #     5
    #     3
    #     3
    #     3
    #     3
    #     3
    #     2
    #     2
    #     2
    #     2
    #     2
    #     2
    #     2
    #     2
    #     1
    #     1
    #     1
    #     1
    #     1
    #
    #---------------------------------------

### Output files for usage example 3

### File: hsfau.restrict

    ########################################
    # Program: restrict
    # Rundate: Thu May 22 15:02:58 2003
    # Report_format: table
    # Report_file: hsfau.restrict
    ########################################

    #=======================================
    #
    # Sequence: HSFAU     from: 1   to: 518
    # HitCount: 53
    #
    # Minimum cuts per enzyme: 1
    # Maximum cuts per enzyme: 2000000000
    # Minimum length of recognition site: 4
    # Blunt ends allowed
    # Sticky ends allowed
    # DNA is linear
    # Ambiguities allowed
    #
    #=======================================

      Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
         11      14 TaqI        TCGA                 11     13         .         .
         28      31 AciI        CCGC                 25     27         .         .
         38      41 AciI        CCGC                 38     40         .         .
         44      48 BceAI       ACGGC                25     27         .         .
         71      74 AciI        CCGC                 71     73         .         .
         71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
         73      76 Hin6I       GCGC                 73     75         .         .
         73      76 HhaI        GCGC                 75     73         .         .
         77      81 BssKI       CCNGG                76     81         .         .
         77      81 EcoRII      CCWGG                76     81         .         .
         94      97 TaqI        TCGA                 94     96         .         .
        103     106 HpaII       CCGG                103    105         .         .
        105     108 HaeIII      GGCC                106    106         .         .
        107     111 EcoRII      CCWGG               106    111         .         .
        107     117 BsiYI       CCNNNNNNNGG         113    110         .         .
        107     111 BssKI       CCNGG               106    111         .         .
        122     132 BsiYI       CCNNNNNNNGG         128    125         .         .
        125     135 Hin4I       GAYNNNNNVTC         116    111       148       143
        146     150 BsrI        ACTGG               151    149         .         .
        161     165 BssKI       CCNGG               160    165         .         .
        162     165 HpaII       CCGG                162    164         .         .
        182     186 BssKI       CCNGG               181    186         .         .
        182     186 EcoRII      CCWGG               181    186         .         .
        190     193 HhaI        GCGC                192    190         .         .
        190     193 Hin6I       GCGC                190    192         .         .
        192     195 HhaI        GCGC                194    192         .         .
        192     195 Hin6I       GCGC                192    194         .         .

      [Part of this file has been deleted for brevity]

    # [ACTGG]
    # 	15	36	77	95	99	196
    #
    # BsrI:
    # [CCNGG]
    # 	70	151	297
    #
    # BssKI:
    # [CCWGG]
    # 	15	21	30	45	51	54
    # 	76	226
    #
    # EcoRII:
    # [GGCC]
    # 	15	30	45	51	75	76
    # 	226
    #
    # HaeIII:
    # [GCGC]
    # 	10	17	25	35	39	79
    # 	103	104	106
    #
    # HhaI:
    # [GAYNNNNNVTC]
    # 	2	75	117	118	206
    #
    # Hin4I:
    # [GCGC]
    # 	32	116	370
    #
    # Hin6I:
    # [GTYRAC]
    # 	2	73	117	120	206
    #
    # HindII:
    # [CCGG]
    # 	111	407
    #
    # HpaII:
    # [ACGT]
    # 	59	103	123	233
    #
    # MaeII:
    # [TCGA]
    # 	109	409
    #
    # TaqI:
    # [TCGA]
    # 	11	83	424
    #
    #---------------------------------------

The output from restrict is a simple text one. The base number, restriction enzyme name, recognition site and cut positions are shown. Note that cuts are always to the right of the residue shown and that 5' cuts are referred to by their associated 3' number sequence.

The program reports enzymes that cut at two or four sites. The program also reports isoschizomers and enzymes having the same recognition sequence but different cut sites.

When the "-fragments" or "-solofragments" qualifiers are given then the sizes of the fragments produced by either all of the specified enzymes cutting, or by each enzyme cutting individually, are given in the 'tail' section at the end of the report file.

## 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

Output file size is related to the size of the recognition site and the maximum number of allowed cutting positions. Setting the site length to six and restricting the cuts to two is a common choice of parameters. The size of the output can sometimes be reduced by specifying the -noambiguity switch.

The data files must have been created before running this program. This is done by running the rebaseextract program with the "withrefm" and "prot" files from an REBASE release. You may have to ask your system manager to do this.

## References

1. Nucleic Acids Research 27: 312-313 (1999).

## Warnings

The program will warn you if a protein sequence is given.

## Diagnostic Error Messages

None.

## Exit status

It exits with status 0 unless an error is reported.

## Known bugs

None.

## See also

Program name | Description
--- | ---
recoder | Remove restriction sites but maintain the same translation
redata | Search REBASE for enzyme name, references, suppliers etc
remap | Display a sequence with restriction cut sites, translation etc
restover | Finds restriction enzymes that produce a specific overhang
showseq | Display a sequence with features, translation etc
silent | Silent mutation restriction enzyme scan

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

Completed 16th April 1999

## Target users

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

## Comments