Tehdyt toimenpiteet
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restrict |
Wiki
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Function
Report restriction enzyme cleavage sites in a nucleotide sequenceDescription
restrict scans one or more nucleotide sequences for cut sites for a supplied set of restriction enzymes. One or more restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. The minimum length of a recognition site to be reported must be specified. It writes an output file showing the location of the cut sites. There are several options to control exactly what sites are reported and the format of the output file. Optionally, the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on its own, or by using all of the input enzymes together, may be reported. Results are added to the tail section of the report.
Algorithm
Usage
Here is a sample session with restrict
% restrict Report restriction enzyme cleavage sites in a nucleotide sequence Input nucleotide sequence(s): tembl:x65923 Minimum recognition site length [4]: Comma separated enzyme list [all]: Output report [x65923.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 Report restriction enzyme cleavage sites in a nucleotide sequence Input nucleotide sequence(s): tembl:x65923 Minimum recognition site length [4]: Comma separated enzyme list [all]: Output report [x65923.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 Report restriction enzyme cleavage sites in a nucleotide sequence Input nucleotide sequence(s): tembl:x65923 Minimum recognition site length [4]: Comma separated enzyme list [all]: Output report [x65923.restrict]: |
Go to the output files for this example
Command line arguments
Report restriction enzyme cleavage sites in a nucleotide sequence
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-sitelen integer [4] 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)
-enzymes string [all] 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)
[-outfile] report [*.restrict] Output report file name
(default -rformat table)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-datafile datafile Restriction enzyme data file (optional)
-mfile datafile [Emethylsites.dat] Restriction enzyme
methylation data file
-min integer [1] 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)
-max integer [2000000000] 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. (Any
integer value)
-solofragment boolean [N] 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 [N] 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 [Y] This allows those enzymes which cut at
the same position on the forward and reverse
strands to be considered.
-[no]sticky boolean [Y] This allows those enzymes which cut at
different positions on the forward and
reverse strands, leaving an overhang, to be
considered.
-[no]ambiguity boolean [Y] This allows those enzymes which have one
or more 'N' ambiguity codes in their
pattern to be considered
-plasmid boolean [N] If this is set then this allows searches
for restriction enzyme recognition site and
cut positions that span the end of the
sequence to be considered.
-methylation boolean [N] If this is set then RE recognition sites
will not match methylated bases.
-[no]commercial boolean [Y] 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 [Y] 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 [N] Sort output alphabetically
-fragments boolean [N] 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 [N] 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
-rstrandshow2 boolean Show the nucleotide strand in the report
-rusashow2 boolean Show the full USA in the report
-rmaxall2 integer Maximum total hits to report
-rmaxseq2 integer Maximum hits to report for one sequence
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to 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 and exit. 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 dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -sitelen | integer | 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 | 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 | Any string | all |
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat table) | <*>.restrict |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -datafile | datafile | Restriction enzyme data file (optional) | Data file | File in the data file path |
| -mfile | datafile | Restriction enzyme methylation data file | Data file | Emethylsites.dat |
| -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. | Integer from 1 to 1000 | 1 |
| -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. | Any integer value | 2000000000 |
| -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. | Boolean value Yes/No | No |
| -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. | Boolean value Yes/No | No |
| -[no]blunt | boolean | 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 | boolean | 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 | boolean | This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered | Boolean value Yes/No | Yes |
| -plasmid | boolean | If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered. | Boolean value Yes/No | No |
| -methylation | boolean | If this is set then RE recognition sites will not match methylated bases. | Boolean value Yes/No | No |
| -[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. | Boolean value Yes/No | Yes |
| -[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. | Boolean value Yes/No | Yes |
| -alphabetic | boolean | Sort output alphabetically | Boolean value Yes/No | No |
| -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. | Boolean value Yes/No | No |
| -name | boolean | Show sequence name | Boolean value Yes/No | No |
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated report qualifiers | ||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | table |
| -rname2 -rname_outfile |
string | Base file name | Any string | |
| -rextension2 -rextension_outfile |
string | File name extension | Any string | |
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | N |
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
Input file format
restrict reads one or more nucleotide sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Input files for usage example
'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:x65923
ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC X65923;
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 11)
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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC 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 PUBMED; 8395683.
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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR H-InvDB; HIT000322806.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /organism="Homo sapiens"
FT /chromosome="11q"
FT /map="13"
FT /mol_type="mRNA"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /tissue_type="placenta"
FT /db_xref="taxon:9606"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /gene="fau"
FT /db_xref="GDB:135476"
FT /db_xref="GOA:P35544"
FT /db_xref="GOA:P62861"
FT /db_xref="HGNC:3597"
FT /db_xref="InterPro:IPR000626"
FT /db_xref="InterPro:IPR006846"
FT /db_xref="InterPro:IPR019954"
FT /db_xref="InterPro:IPR019955"
FT /db_xref="InterPro:IPR019956"
FT /db_xref="UniProtKB/Swiss-Prot:P35544"
FT /db_xref="UniProtKB/Swiss-Prot:P62861"
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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, 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' format report file.
Output files for usage example
File: x65923.restrict
########################################
# Program: restrict
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: restrict
# -sequence tembl:x65923
# Report_format: table
# Report_file: x65923.restrict
########################################
#=======================================
#
# Sequence: X65923 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 Strand Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
11 14 + TaqI TCGA 11 13 . .
25 28 - AciI CCGC 25 27 . .
31 36 - BseYI CCCAGC 31 35 . .
38 41 + AciI CCGC 38 40 . .
40 44 - BceAI ACGGC 25 27 . .
71 81 + BsiYI CCNNNNNNNGG 77 74 . .
71 74 + AciI CCGC 71 73 . .
73 76 + Hin6I GCGC 73 75 . .
73 76 + HhaI GCGC 75 73 . .
77 81 + EcoRII CCWGG 76 81 . .
77 81 + BssKI CCNGG 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 . .
107 111 + BssKI CCNGG 106 111 . .
107 117 + BsiYI CCNNNNNNNGG 113 110 . .
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 + EcoRII CCWGG 181 186 . .
182 186 + BssKI CCNGG 181 186 . .
190 193 + Hin6I GCGC 190 192 . .
190 193 + HhaI GCGC 192 190 . .
192 195 + Hin6I GCGC 192 194 . .
192 195 + HhaI GCGC 194 192 . .
197 201 + EcoRII CCWGG 196 201 . .
197 201 + BssKI CCNGG 196 201 . .
209 212 + HaeIII GGCC 210 210 . .
219 222 + HaeIII GGCC 220 220 . .
221 231 + BsiYI CCNNNNNNNGG 227 224 . .
221 225 - BsrI ACTGG 221 219 . .
226 229 - AciI CCGC 226 228 . .
236 239 + HaeIII GGCC 237 237 . .
248 252 + EcoRII CCWGG 247 252 . .
248 252 + BssKI CCNGG 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 . .
377 380 - AciI CCGC 377 379 . .
380 383 - AciI CCGC 380 382 . .
395 398 + HpaII CCGG 395 397 . .
398 401 + Hin6I GCGC 398 400 . .
398 401 + HhaI GCGC 400 398 . .
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 . .
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_length: 518
# Reported_sequences: 1
# Reported_hitcount: 54
#---------------------------------------
|
Output files for usage example 2
File: x65923.restrict
########################################
# Program: restrict
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: restrict
# -fragments
# -sequence tembl:x65923
# Report_format: table
# Report_file: x65923.restrict
########################################
#=======================================
#
# Sequence: X65923 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 Strand Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
11 14 + TaqI TCGA 11 13 . .
25 28 - AciI CCGC 25 27 . .
31 36 - BseYI CCCAGC 31 35 . .
38 41 + AciI CCGC 38 40 . .
40 44 - BceAI ACGGC 25 27 . .
71 81 + BsiYI CCNNNNNNNGG 77 74 . .
71 74 + AciI CCGC 71 73 . .
73 76 + Hin6I GCGC 73 75 . .
73 76 + HhaI GCGC 75 73 . .
77 81 + EcoRII CCWGG 76 81 . .
77 81 + BssKI CCNGG 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 . .
107 111 + BssKI CCNGG 106 111 . .
107 117 + BsiYI CCNNNNNNNGG 113 110 . .
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 + EcoRII CCWGG 181 186 . .
182 186 + BssKI CCNGG 181 186 . .
[Part of this file has been deleted for brevity]
# 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
#
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_length: 518
# Reported_sequences: 1
# Reported_hitcount: 54
#---------------------------------------
|
Output files for usage example 3
File: x65923.restrict
########################################
# Program: restrict
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: restrict
# -solofragment
# -sequence tembl:x65923
# Report_format: table
# Report_file: x65923.restrict
########################################
#=======================================
#
# Sequence: X65923 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 Strand Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
11 14 + TaqI TCGA 11 13 . .
25 28 - AciI CCGC 25 27 . .
31 36 - BseYI CCCAGC 31 35 . .
38 41 + AciI CCGC 38 40 . .
40 44 - BceAI ACGGC 25 27 . .
71 81 + BsiYI CCNNNNNNNGG 77 74 . .
71 74 + AciI CCGC 71 73 . .
73 76 + Hin6I GCGC 73 75 . .
73 76 + HhaI GCGC 75 73 . .
77 81 + EcoRII CCWGG 76 81 . .
77 81 + BssKI CCNGG 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 . .
107 111 + BssKI CCNGG 106 111 . .
107 117 + BsiYI CCNNNNNNNGG 113 110 . .
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 + EcoRII CCWGG 181 186 . .
182 186 + BssKI CCNGG 181 186 . .
[Part of this file has been deleted for brevity]
# 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
#
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_length: 518
# Reported_sequences: 1
# Reported_hitcount: 54
#---------------------------------------
|
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 in 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 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
Several criteria may be set to control what sites are reported: -min, -max, -single (minimum or maximum number of cuts, or single site cuts only. -blunt (enzymes which cut at the same position on the forward and reverse strands). -sticky (enzymes which cut at different positions on the forward and reverse strands, leaving an overhang). -ambiguity (enzymes which have one or more N ambiguity codes in their pattern). -commercial (enzymes with a commercial supplier). -plasmid (allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence).
By default, only one enzyme of any group of isoschizomers (enzymes that have the same recognition site and cut positions) is reported. This behaviour can be changed by specifying -nolimit, in which case all isoschizomers are reported. The default behaviour uses the representative enzyme of an isoschizomer group (the prototype) which is specified in the EMBOSS data file embossre.equ. This file is generated from the REBASE database by running rebaseextract. You may edit this file to set your own preferred prototype,if you wish.
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.
References
- Nucleic Acids Research 27: 312-313 (1999).
Warnings
restrict uses the EMBOSS REBASE restriction enzyme data files stored in 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.
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 | Find restriction sites to remove (mutate) with no translation change |
| redata | Retrieve information from REBASE restriction enzyme database |
| remap | Display restriction enzyme binding sites in a nucleotide sequence |
| restover | Find restriction enzymes producing a specific overhang |
| showseq | Displays sequences with features in pretty format |
| silent | Find restriction sites to insert (mutate) with no translation change |
Author(s)
Alan BleasbyEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.