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restrict |
% restrict Finds restriction enzyme cleavage sites Input sequence(s): embl:hsfau Minimum recognition site length [4]: Comma separated enzyme list [all]: Output file [hsfau.restrict]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -sitelen integer Minimum recognition site length -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 Minimum cuts per RE -max integer Maximum cuts per RE -single boolean Force single site only cuts -[no]blunt boolean Allow blunt end cutters -[no]sticky boolean Allow sticky end cutters -[no]ambiguity boolean Allow ambiguous matches -plasmid boolean Allow circular DNA -[no]commercial boolean Only enzymes with suppliers -datafile string Alternative RE data file -[no]limit boolean Limits reports to one isoschizomer -preferred boolean Report preferred isoschizomers -alphabetic boolean Sort output alphabetically -fragments boolean Show fragment lengths -name boolean Show sequence name General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-sitelen | Minimum recognition site length | 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 file | |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-min | Minimum cuts per RE | Integer from 1 to 1000 | 1 |
-max | Maximum cuts per RE | Integer up to 2000000000 | 2000000000 |
-single | Force single site only cuts | Yes/No | No |
-[no]blunt | Allow blunt end cutters | Yes/No | Yes |
-[no]sticky | Allow sticky end cutters | Yes/No | Yes |
-[no]ambiguity | Allow ambiguous matches | Yes/No | Yes |
-plasmid | Allow circular DNA | Yes/No | No |
-[no]commercial | Only enzymes with suppliers | Yes/No | Yes |
-datafile | Alternative RE data file | Any string is accepted | An empty string is accepted |
-[no]limit | Limits reports to one isoschizomer | Yes/No | Yes |
-preferred | Report preferred isoschizomers | Yes/No | No |
-alphabetic | Sort output alphabetically | Yes/No | No |
-fragments | Show fragment lengths | Yes/No | No |
-name | Show sequence name | Yes/No | No |
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.
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.
Here is part of a sample output:
######################################## # Program: restrict # Rundate: Mon Feb 11 13:46:44 2002 # Report_file: hsfau.restrict ######################################## #======================================= # # Sequence: HSFAU from: 1 to: 518 # HitCount: 214 # # 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 # # #======================================= USA Start End Score Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev HSFAU 3 6 0.000 MnlI CCTC 13 12 . . HSFAU 9 14 0.000 Hpy188III TCNNGA 10 12 . . HSFAU 11 14 0.000 TaqI TCGA 11 13 . . HSFAU 13 17 0.000 HinfI GANTC 13 16 . . HSFAU 17 21 0.000 MlyI GAGTC 7 7 . . HSFAU 17 21 0.000 PleI GAGTC 7 8 . . HSFAU 24 27 0.000 AccII CGCG 25 25 . . HSFAU 24 28 0.000 MboII GAAGA 12 11 . . HSFAU 28 31 0.000 AciI CCGC 25 27 . . etc. HSFAU 437 443 0.000 DraII RGGNCCY 438 441 . . HSFAU 438 442 0.000 AspS9I GGNCC 438 441 . . HSFAU 438 443 0.000 BscBI GGNNCC 440 440 . . HSFAU 438 441 0.000 BshFI GGCC 439 439 . . HSFAU 438 441 0.000 CviJI RGCY 439 439 . . HSFAU 454 459 0.000 AflII CTTAAG 454 458 . . HSFAU 454 459 0.000 SmlI CTYRAG 454 458 . . HSFAU 455 458 0.000 MseI TTAA 455 457 . . HSFAU 468 471 0.000 Sse9I AATT 467 471 . . HSFAU 474 477 0.000 CviJI RGCY 475 475 . . HSFAU 492 495 0.000 CviJI RGCY 493 493 . . HSFAU 497 501 0.000 BstDEI CTNAG 497 500 . . #--------------------------------------- #---------------------------------------
The data files must have been created before running this program. This is done by running the rebaseextract program with the "withrefm" file from an REBASE release. You may have to ask your system manager to do this.
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 |