                                   recoder



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Function

   Find restriction sites to remove (mutate) with no translation change

Description

   recoder finds restriction enzyme sites in a nucleotide sequence which
   can be removed without changing the translation. recoder scans a
   nucleotide sequence for restriction sites for a supplied set of
   restriction enzymes. It writes a standard EMBOSS report of single base
   positions which, when mutated, remove the restriction site whilst
   maintaining the same translation in frame 1 of the input sequence. One
   or more restriction enzymes can be specified or alternatively all the
   enzymes in the REBASE database can be investigated. Optionally, the
   untranslated and translated sequence may be reported.

Usage

   Here is a sample session with recoder


% recoder
Find restriction sites to remove (mutate) with no translation change
Input nucleotide sequence: tembl:x65923
Comma separated enzyme list [all]: EcoRII
Output report [x65923.recoder]:


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

Command line arguments

Find restriction sites to remove (mutate) with no translation change
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
   -enzymes            string     [all] Comma separated enzyme list (Any
                                  string)
  [-outfile]           report     [*.recoder] Output report file name (default
                                  -rformat table)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -sshow              boolean    [N] Display untranslated sequence
   -tshow              boolean    [N] Display translated sequence

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   recoder reads a single nucleotide sequence.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  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 INSDC.
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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
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="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
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
//

Output file format

   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, dasgff, debug, listfile, dbmotif, diffseq,
   draw, restrict, excel, feattable, motif, nametable, regions, seqtable,
   simple, srs, table, tagseq.

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default, the output is in 'table' format.

  Output files for usage example

  File: x65923.recoder

########################################
# Program: recoder
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: recoder
#    -sequence tembl:x65923
#    -enzymes EcoRII
# Report_format: table
# Report_file: x65923.recoder
########################################

#=======================================
#
# Sequence: X65923     from: 1   to: 518
# HitCount: 22
#
# KEY:
# EnzymeName: Enzyme name
# RS-Pattern: Restriction enzyme recognition site pattern
# Base-Posn: Position of base to be mutated
# AAs: Amino acid. Original sequence(.)After mutation
# Mutation: The base mutation to perform
#
# Creating silent mutations
#
#=======================================

  Start     End  Strand EnzymeName RS-Pattern Base-Posn    AAs Mutation
     77      81       + EcoRII     CCWGG             78    P.P     C->G
     77      81       + EcoRII     CCWGG             78    P.P     C->A
     77      81       + EcoRII     CCWGG             78    P.P     C->T
     77      81       + EcoRII     CCWGG             79    R.R     A->C
     77      81       + EcoRII     CCWGG             81    R.R     G->A
    107     111       + EcoRII     CCWGG            108    A.A     C->G
    107     111       + EcoRII     CCWGG            108    A.A     C->A
    107     111       + EcoRII     CCWGG            108    A.A     C->T
    107     111       + EcoRII     CCWGG            109    R.R     A->C
    107     111       + EcoRII     CCWGG            111    R.R     G->A
    182     186       + EcoRII     CCWGG            183    S.S     C->G
    182     186       + EcoRII     CCWGG            183    S.S     C->A
    182     186       + EcoRII     CCWGG            183    S.S     C->T
    197     201       + EcoRII     CCWGG            198    P.P     C->G
    197     201       + EcoRII     CCWGG            198    P.P     C->A
    197     201       + EcoRII     CCWGG            198    P.P     C->T
    248     252       + EcoRII     CCWGG            249    P.P     C->G
    248     252       + EcoRII     CCWGG            249    P.P     C->A
    248     252       + EcoRII     CCWGG            249    P.P     C->T
    293     297       + EcoRII     CCWGG            294    P.P     C->G
    293     297       + EcoRII     CCWGG            294    P.P     C->A
    293     297       + EcoRII     CCWGG            294    P.P     C->T

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_length: 518
# Reported_sequences: 1
# Reported_hitcount: 22
#---------------------------------------

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

   To find out whether the single point mutations found by recoder
   introduce new restriction sites, silent should be run on the original
   sequence. silent does the opposite to recoder. silent finds sites where
   a restriction enzyme site can be introduced without changing the
   translation in frame 1 of the sequence.

References

   None.

Warnings

   recoder 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
   redata           Retrieve information from REBASE restriction enzyme database
   remap            Display restriction enzyme binding sites in a nucleotide sequence
   restover         Find restriction enzymes producing a specific overhang
   restrict         Report restriction enzyme cleavage sites in a nucleotide
                    sequence
   showseq          Display sequences with features in pretty format
   silent           Find restriction sites to insert (mutate) with no translation
                    change

   silent does the opposite to recoder. silent finds sites where a
   restriction enzyme site can be introduced without changing the
   translation in frame 1 of the sequence. recoder finds sites where a
   restriction enzyme site can be removed without changing the translation
   in frame 1 of the sequence.

Author(s)

   Tim Carver formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written (January 2001) - Tim Carver

   Renamed from recode to recoder 16 May 2001 as the old name clashed with
   a common UNIX print utility:
   http://www.iro.umontreal.ca/contrib/recode/HTML/

Target users

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

Comments

   None
