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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
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 output 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 | Boolean value Yes/No | No |
-[no]blunt | Allow blunt end cutters | Boolean value Yes/No | Yes |
-[no]sticky | Allow sticky end cutters | Boolean value Yes/No | Yes |
-[no]ambiguity | Allow ambiguous matches | Boolean value Yes/No | Yes |
-plasmid | Allow circular DNA | Boolean value Yes/No | No |
-[no]commercial | Only enzymes with suppliers | Boolean value Yes/No | Yes |
-datafile | Alternative RE data file | Any string is accepted | An empty string is accepted |
-[no]limit | Limits reports to one isoschizomer | Boolean value Yes/No | Yes |
-preferred | Report preferred isoschizomers | Boolean value Yes/No | No |
-alphabetic | Sort output alphabetically | Boolean value Yes/No | No |
-fragments | Show fragment lengths | Boolean value Yes/No | No |
-name | Show sequence name | Boolean value Yes/No | No |
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 // |
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.
######################################## # Program: restrict # Rundate: Thu Nov 07 14:42:26 2002 # 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 Score Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev 11 14 0 TaqI TCGA 11 13 . . 28 31 0 AciI CCGC 25 27 . . 38 41 0 AciI CCGC 38 40 . . 44 48 0 BceAI ACGGC 25 27 . . 71 74 0 AciI CCGC 71 73 . . 71 81 0 Bsc4I CCNNNNNNNGG 77 74 . . 73 76 0 HhaI GCGC 75 73 . . 73 76 0 Hin6I GCGC 73 75 . . 77 81 0 BssKI CCNGG 76 81 . . 77 81 0 EcoRII CCWGG 76 81 . . 94 97 0 TaqI TCGA 94 96 . . 103 106 0 BsiSI CCGG 103 105 . . 105 108 0 BshI GGCC 106 106 . . 107 117 0 Bsc4I CCNNNNNNNGG 113 110 . . 107 111 0 BssKI CCNGG 106 111 . . 107 111 0 EcoRII CCWGG 106 111 . . 122 132 0 Bsc4I CCNNNNNNNGG 128 125 . . 125 135 0 Hin4I GAYNNNNNVTC 116 111 148 143 146 150 0 Bse1I ACTGG 151 149 . . 161 165 0 BssKI CCNGG 160 165 . . 162 165 0 BsiSI CCGG 162 164 . . 182 186 0 BssKI CCNGG 181 186 . . 182 186 0 EcoRII CCWGG 181 186 . . 190 193 0 HhaI GCGC 192 190 . . 190 193 0 Hin6I GCGC 190 192 . . 192 195 0 Hin6I GCGC 192 194 . . 192 195 0 HhaI GCGC 194 192 . . 197 201 0 BssKI CCNGG 196 201 . . 197 201 0 EcoRII CCWGG 196 201 . . 209 212 0 BshI GGCC 210 210 . . 219 222 0 BshI GGCC 220 220 . . 221 231 0 Bsc4I CCNNNNNNNGG 227 224 . . 225 229 0 Bse1I ACTGG 221 219 . . 229 232 0 AciI CCGC 226 228 . . 236 239 0 BshI GGCC 237 237 . . 248 252 0 BssKI CCNGG 247 252 . . 248 252 0 EcoRII CCWGG 247 252 . . 261 264 0 BshI GGCC 262 262 . . 263 266 0 AciI CCGC 263 265 . . 293 297 0 BssKI CCNGG 292 297 . . 293 297 0 EcoRII CCWGG 292 297 . . 296 299 0 BshI GGCC 297 297 . . 335 338 0 BshI GGCC 336 336 . . 380 383 0 AciI CCGC 377 379 . . 383 386 0 AciI CCGC 380 382 . . 395 398 0 BsiSI CCGG 395 397 . . 398 401 0 HhaI GCGC 400 398 . . 398 401 0 Hin6I GCGC 398 400 . . 405 410 0 HindII GTYRAC 407 407 . . 408 413 0 AclI AACGTT 409 411 . . 409 412 0 HpyCH4IV ACGT 409 411 . . 417 427 0 Bsc4I CCNNNNNNNGG 423 420 . . 438 441 0 BshI GGCC 439 439 . . #--------------------------------------- #--------------------------------------- |
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.
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 |