
                                 restover 



Function

   Find restriction enzymes producing a specific overhang

Description

   restover identifies restriction enzymes from the REBASE database that
   create the specified overhang sequence when they cut the input
   nucleotide sequence(s). It writes an output file which shows the base
   number, restriction enzyme name, recognition site and cut positions.
   There are several options to control exactly what sites are reported
   and the format of the output file. Optionally, output in HTML may be
   generated.

Usage

   Here is a sample session with restover


% restover 
Find restriction enzymes producing a specific overhang
Input nucleotide sequence(s): tembl:x65923
Overlap sequence: cg
Output file [x65923.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     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-seqcomp]           string     Overlap sequence (Any string is accepted)
  [-outfile]           outfile    [*.restover] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -datafile           datafile   Restriction enzyme data file (optional)
   -min                integer    [1] Minimum cuts per RE (Integer from 1 to
                                  1000)
   -max                integer    [2000000000] Maximum cuts per RE (Integer up
                                  to 2000000000)
   -single             boolean    [N] Force single site only cuts
   -threeprime         boolean    [N] Use 3' overhang e.g. BamHI has CTAG as a
                                  5' overhang, and ApaI has CCGG as 3'
                                  overhang.
   -[no]blunt          boolean    [Y] Allow blunt end cutters
   -[no]sticky         boolean    [Y] Allow sticky end cutters
   -[no]ambiguity      boolean    [Y] Allow ambiguous matches
   -plasmid            boolean    [N] Allow circular DNA
   -[no]commercial     boolean    [Y] Only enzymes with suppliers
   -html               boolean    [N] Create HTML output
   -[no]limit          boolean    [Y] Limits reports to one isoschizomer
   -alphabetic         boolean    [N] Sort output alphabetically
   -fragments          boolean    [N] Show fragment lengths

   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 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. 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

Input file format

   restover reads in a normal nucleic acid sequence USA.

  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 sequences 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="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
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: x65923.restover

# Restrict of X65923 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 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 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 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/

   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.

References

   None.

Warnings

   restover 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 always exits with status 0.

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
   restrict Report restriction enzyme cleavage sites in a nucleotide
   sequence
   showseq Displays sequences with features in pretty format
   silent Find restriction sites to insert (mutate) with no translation
   change

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
