
                                 restover 



Function

   Finds restriction enzymes that produce a specific overhang

Description

   The Restriction Enzyme database (REBASE) is a collection of
   information about restriction enzymes and related proteins. It
   contains published and unpublished references, recognition and
   cleavage sites, isoschizomers, commercial availability, methylation
   sensitivity, crystal and sequence data. DNA methyltransferases, homing
   endonucleases, nicking enzymes, specificity subunits and control
   proteins are also included. Most recently, putative DNA
   methyltransferases and restriction enzymes, as predicted from analysis
   of genomic sequences, are also listed.

   The home page of REBASE is: http://rebase.neb.com/

   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.

Usage

   Here is a sample session with restover


% restover 
Finds restriction enzymes that produce a specific overhang
Input sequence(s): tembl:hsfau
Overlap sequence: cg
Output file [hsfau.restover]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-seqcomp]           string     Overlap sequence
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -datafile           datafile   Alternative RE data file
   -min                integer    Minimum cuts per RE
   -max                integer    Maximum cuts per RE
   -single             boolean    Force single site only cuts
   -threeprime         boolean    Use 3' overhang e.g. BamHI has CTAG as a 5'
                                  overhang, and ApaI has CCGG as 3' overhang.
   -[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
   -html               boolean    Create HTML output
   -[no]limit          boolean    Limits reports to one isoschizomer
   -alphabetic         boolean    Sort output alphabetically
   -fragments          boolean    Show fragment lengths
   -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
   -odirectory3         string     Output directory

   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
   [-seqcomp]
   (Parameter 2) Overlap sequence Any string is accepted An empty string
   is accepted
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.restover
   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 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
   -threeprime Use 3' overhang e.g. BamHI has CTAG as a 5' overhang, and
   ApaI has CCGG as 3' overhang. 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
   -html Create HTML output Boolean value Yes/No No
   -[no]limit Limits reports to one isoschizomer Boolean value Yes/No Yes
   -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

Input file format

   restover reads in a normal nucleic acid sequence USA.

  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

  Output files for usage example

  File: hsfau.restover

# 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: 54
# Base Number   Enzyme          Site            5'      3'      [5'     3']
        11      TaqI            TCGA            11      13
        28      AciI            CCGC            25      27
        38      AciI            CCGC            38      40
        44      BceAI           ACGGC           25      27
        71      AciI            CCGC            71      73
        73      Hin6I           GCGC            73      75
        94      TaqI            TCGA            94      96
        103     HpaII           CCGG            103     105
        162     HpaII           CCGG            162     164
        190     Hin6I           GCGC            190     192
        192     Hin6I           GCGC            192     194
        225     BsrI            ACTGG           221     219
        229     AciI            CCGC            226     228
        263     AciI            CCGC            263     265
        380     AciI            CCGC            377     379
        383     AciI            CCGC            380     382
        395     HpaII           CCGG            395     397
        398     Hin6I           GCGC            398     400
        408     AclI            AACGTT          409     411
        409     MaeII           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.

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

   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.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

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
   restrict     Finds restriction enzyme cleavage sites
   showseq      Display a sequence with features, translation etc
   silent       Silent mutation restriction enzyme scan

Author(s)

   Bernd Jagla (bernd © golgi.ski.mskcc.org)
   Cellular Biochemistry and Biophysics Program, Rockefeller Research
   Laboratories, Memorial Sloan-Kettering Cancer Center, 1275 York
   Avenue, Box 251,New York, NY 10021.

History

   Written (Jan 2001) - Bernd Jagla

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
