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EMBOSS: restover |
The home page of REBASE is: http://rebase.neb.com/rebase/rebase.html
restover takes a specified sequence and a short sequence of a cut-site overhang and searches the REBASE database for matching enzymes that create the desired overhang sequence when they cut the input sequence.
% restover Finds restriction enzymes that produce a specific overhang Input sequence(s): em:hsfau Overlap sequence: cg Output file [hsfau.restover]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-seqcomp] string Overlap sequence [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -min integer Minimum cuts per RE -max integer Maximum cuts per RE -single bool Force single site only cuts -threeprime bool 3' overhang? (else 5') e.g. BamHI has CTAG as a 5' overhang, and ApaI has CCGG as 3' overhang. -html bool Create HTML output -[no]blunt bool Allow blunt end cutters -[no]sticky bool Allow sticky end cutters -[no]ambiguity bool Allow ambiguous matches -plasmid bool Allow circular DNA -[no]commercial bool Only enzymes with suppliers -[no]limit bool Limits reports to one isoschizomer -preferred bool Report preferred isoschizomers -alphabetic bool Sort output alphabetically -fragments bool Show fragment lengths -name bool Show sequence name -datafile string Alternative RE data file General qualifiers: -help bool 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 |
[-seqcomp] (Parameter 2) |
Overlap sequence | Any string is accepted | An empty string is accepted |
[-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.restover |
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 |
-threeprime | 3' overhang? (else 5') e.g. BamHI has CTAG as a 5' overhang, and ApaI has CCGG as 3' overhang. | Yes/No | No |
-html | Create HTML output | 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 |
-[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 |
-datafile | Alternative RE data file | Any string is accepted | An empty string is accepted |
# Restrict of HSFAU from 1 to 518 # # Minimum cuts per enzyme: 1 # Maximum cuts per enzyme: 2000000000 # Minimum length of recognition site: 2 # Number of hits with any overlap: 208 # Base Number Enzyme Site 5' 3' [5' 3'] 11 TaqI TCGA 11 13 28 AciI CCGC 25 27 38 AciI CCGC 38 40 71 AciI CCGC 71 73 73 Hin6I GCGC 73 75 94 TaqI TCGA 94 96 103 BsiSI CCGG 103 105 162 BsiSI CCGG 162 164 190 Hin6I GCGC 190 192 192 Hin6I GCGC 192 194 225 Bse1I ACTGG 221 219 229 AciI CCGC 226 228 263 AciI CCGC 263 265 380 AciI CCGC 377 379 383 AciI CCGC 380 382 395 BsiSI CCGG 395 397 398 Hin6I GCGC 398 400 408 AclI AACGTT 409 411 409 HpyCH4IV ACGT 409 411
The output from restover 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 column information is described at the top of the data files
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 |
restrict | Finds restriction enzyme cleavage sites |
showseq | Display a sequence with features, translation etc |
silent | Silent mutation restriction enzyme scan |