
                                 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

   Standard (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

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -datafile           datafile   Alternative RE data file
   -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
                                  its 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.
   -[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" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -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
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated 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 standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -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


   Standard (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
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -datafile Alternative RE data file Data file File in the data file
   path
   -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
   its 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
   -[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="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
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        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

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://emboss.sf.net/docs/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 Jul 15 2004 12:00:00
# Report_format: table
# Report_file: hsfau.restrict
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 54
#
# 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      25 AciI        CCGC                 25     27         .         .
     36      31 BseYI       CCCAGC               31     35         .         .
     38      41 AciI        CCGC                 38     40         .         .
     44      40 BceAI       ACGGC                25     27         .         .
     71      74 AciI        CCGC                 71     73         .         .
     71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
     73      76 HhaI        GCGC                 75     73         .         .
     73      76 Hin6I       GCGC                 73     75         .         .
     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     117 BsiYI       CCNNNNNNNGG         113    110         .         .
    107     111 BssKI       CCNGG               106    111         .         .
    107     111 EcoRII      CCWGG               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 Hin6I       GCGC                192    194         .         .
    192     195 HhaI        GCGC                194    192         .         .
    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     221 BsrI        ACTGG               221    219         .         .
    229     226 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 BssKI       CCNGG               292    297         .         .
    293     297 EcoRII      CCWGG               292    297         .         .
    296     299 HaeIII      GGCC                297    297         .         .
    335     338 HaeIII      GGCC                336    336         .         .
    380     377 AciI        CCGC                377    379         .         .
    383     380 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 Jul 15 2004 12:00:00
# Report_format: table
# Report_file: hsfau.restrict
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 54
#
# 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      25 AciI        CCGC                 25     27         .         .
     36      31 BseYI       CCCAGC               31     35         .         .
     38      41 AciI        CCGC                 38     40         .         .
     44      40 BceAI       ACGGC                25     27         .         .
     71      74 AciI        CCGC                 71     73         .         .
     71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
     73      76 HhaI        GCGC                 75     73         .         .
     73      76 Hin6I       GCGC                 73     75         .         .
     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     117 BsiYI       CCNNNNNNNGG         113    110         .         .
    107     111 BssKI       CCNGG               106    111         .         .
    107     111 EcoRII      CCWGG               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 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
#     12
#     11
#     10
#     10
#     10
#     9
#     9
#     9
#     7
#     7
#     7
#     6
#     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 Jul 15 2004 12:00:00
# Report_format: table
# Report_file: hsfau.restrict
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 54
#
# 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      25 AciI        CCGC                 25     27         .         .
     36      31 BseYI       CCCAGC               31     35         .         .
     38      41 AciI        CCGC                 38     40         .         .
     44      40 BceAI       ACGGC                25     27         .         .
     71      74 AciI        CCGC                 71     73         .         .
     71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
     73      76 HhaI        GCGC                 75     73         .         .
     73      76 Hin6I       GCGC                 73     75         .         .
     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     117 BsiYI       CCNNNNNNNGG         113    110         .         .
    107     111 BssKI       CCNGG               106    111         .         .
    107     111 EcoRII      CCWGG               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 Hin6I       GCGC                192    194         .         .


  [Part of this file has been deleted for brevity]

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

   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 EMBOSS REBASE restriction enzyme data files are stored iin
   directory '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.

   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 © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   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

   None
