restrict.txt

emboss的linux版本的源代码

#     5
#     5
#     3
#     3
#     3
#     3
#     3
#     2
#     2
#     2
#     2
#     2
#     2
#     2
#     2
#     1
#     1
#     1
#     1
#     1
#
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 54
#---------------------------------------

  Output files for usage example 3

  File: hsfau.restrict

########################################
# Program: restrict
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: restrict
#    -solofragment
#    -sequence tembl:hsfau
# Report_format: table
# Report_file: hsfau.restrict
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 54
#
# 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 Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
     11      14 TaqI        TCGA                 11     13         .         .
     28      25 AciI        CCGC                 25     27         .         .
     36      31 BseYI       CCCAGC               31     35         .         .
     38      41 AciI        CCGC                 38     40         .         .
     44      40 BceAI       ACGGC                25     27         .         .
     71      81 BsiYI       CCNNNNNNNGG          77     74         .         .
     71      74 AciI        CCGC                 71     73         .         .
     73      76 Hin6I       GCGC                 73     75         .         .
     73      76 HhaI        GCGC                 75     73         .         .
     77      81 EcoRII      CCWGG                76     81         .         .
     77      81 BssKI       CCNGG                76     81         .         .
     94      97 TaqI        TCGA                 94     96         .         .
    103     106 HpaII       CCGG                103    105         .         .
    105     108 HaeIII      GGCC                106    106         .         .
    107     111 EcoRII      CCWGG               106    111         .         .
    107     111 BssKI       CCNGG               106    111         .         .
    107     117 BsiYI       CCNNNNNNNGG         113    110         .         .
    122     132 BsiYI       CCNNNNNNNGG         128    125         .         .
    125     135 Hin4I       GAYNNNNNVTC         116    111       148       143
    146     150 BsrI        ACTGG               151    149         .         .
    161     165 BssKI       CCNGG               160    165         .         .
    162     165 HpaII       CCGG                162    164         .         .
    182     186 EcoRII      CCWGG               181    186         .         .
    182     186 BssKI       CCNGG               181    186         .         .


  [Part of this file has been deleted for brevity]

#       70      151     297
#
# BssKI:
# [CCNGG]
#       15      21      30      45      51      54
#       76      226
#
# EcoRII:
# [CCWGG]
#       15      30      45      51      75      76
#       226
#
# HaeIII:
# [GGCC]
#       10      17      25      35      39      79
#       103     104     106
#
# HhaI:
# [GCGC]
#       2       75      117     118     206
#
# Hin4I:
# [GAYNNNNNVTC]
#       32      116     370
#
# Hin6I:
# [GCGC]
#       2       73      117     120     206
#
# HindII:
# [GTYRAC]
#       111     407
#
# HpaII:
# [CCGG]
#       59      103     123     233
#
# MaeII:
# [ACGT]
#       109     409
#
# TaqI:
# [TCGA]
#       11      83      424
#
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 54
#---------------------------------------

   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.

   When the "-fragments" or "-solofragments" qualifiers are given then
   the sizes of the fragments produced by either all of the specified
   enzymes cutting, or by each enzyme cutting individually, are given in
   the 'tail' section at the end of the report file.

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

   Output file size is related to the size of the recognition site and
   the maximum number of allowed cutting positions. Setting the site
   length to six and restricting the cuts to two is a common choice of
   parameters. The size of the output can sometimes be reduced by
   specifying the -noambiguity switch.

   The data files must have been created before running this program.
   This is done by running the rebaseextract program with the "withrefm"
   and "prot" files from an REBASE release. You may have to ask your
   system manager to do this.

References

    1. Nucleic Acids Research 27: 312-313 (1999).

Warnings

   The program will warn you if a protein sequence is given.

Diagnostic Error Messages

   None.

Exit status

   It exits with status 0 unless an error is reported.

Known bugs

   None.

See also

   Program name                       Description
   recoder      Remove restriction sites but maintain same translation
   redata       Search REBASE for enzyme name, references, suppliers etc
   remap        Display sequence with restriction sites, translation etc
   restover     Find restriction enzymes producing specific overhang
   showseq      Display a sequence with features, translation etc
   silent       Silent mutation restriction enzyme scan

Author(s)

   Alan Bleasby (ajb