EMBOSS: recoder manual

recoder

Function

Remove restriction sites but maintain same translation

Description

recoder scans a given nucleotide sequence for restriction sites. It reports single base positions in the restriction pattern which when mutated remove the restriction site whilst maintaining the same translation (in frame 1 of the input sequence).

Several restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. To find out whether the single point mutations found by 'recoder', introduce new restriction sites, 'silent' should be run on the original sequence. ('Silent' searches for silent point mutation sites which maintain the same translation.

The output for 'recoder' is similar to the format used by 'silent'.

Usage

Here is a sample session with recoder


% recoder 
Remove restriction sites but maintain same translation
Input sequence: tembl:hsfau
Comma separated enzyme list [all]: EcoRII
Output report [hsfau.recoder]:

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Sequence USA
   -enzymes            string     Comma separated enzyme list
  [-outfile]           report     Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -sshow              boolean    Display untranslated sequence
   -tshow              boolean    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
   -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
   -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
   -rusashow2           boolean    Show the full USA in the report

   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 USA	Readable sequence	Required
-enzymes	Comma separated enzyme list	Any string is accepted	all
[-outfile] (Parameter 2)	Output report file name	Report output file
Additional (Optional) qualifiers		Allowed values	Default
(none)
Advanced (Unprompted) qualifiers		Allowed values	Default
-sshow	Display untranslated sequence	Boolean value Yes/No	No
-tshow	Display translated sequence	Boolean value Yes/No	No

Input file format

recoder reads 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="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

Output files for usage example

File: hsfau.recoder

########################################
# Program: recoder
# Rundate: Fri Jul 15 2005 12:00:00
# Report_format: table
# Report_file: hsfau.recoder
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 34
#
# KEY:
# Dir: Direction (Rev for reverse complement)
# 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 Dir    EnzymeName RS-Pattern Base-Posn    AAs Mutation
     77      81 .      EcoRII     CCWGG             78    P.P     C->T
     77      81 .      EcoRII     CCWGG             78    P.P     C->G
     77      81 .      EcoRII     CCWGG             78    P.P     C->A
     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->T
    107     111 .      EcoRII     CCWGG            108    A.A     C->G
    107     111 .      EcoRII     CCWGG            108    A.A     C->A
    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
     81      77 Rev    EcoRII     CCWGG             79    P.P     T->C
     81      77 Rev    EcoRII     CCWGG             79    P.P     T->G
    111     107 Rev    EcoRII     CCWGG            109    P.P     T->C
    111     107 Rev    EcoRII     CCWGG            109    P.P     T->G
    186     182 Rev    EcoRII     CCWGG            184    P.P     A->G
    186     182 Rev    EcoRII     CCWGG            184    P.P     A->C
    201     197 Rev    EcoRII     CCWGG            199    P.P     A->C
    201     197 Rev    EcoRII     CCWGG            199    P.P     A->G
    252     248 Rev    EcoRII     CCWGG            250    P.P     A->C
    252     248 Rev    EcoRII     CCWGG            250    P.P     A->G
    297     293 Rev    EcoRII     CCWGG            295    P.P     A->C
    297     293 Rev    EcoRII     CCWGG            295    P.P     A->G

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

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

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

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

Author(s)

Tim Carver (tcarver © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:hsfau

Output file format

Output files for usage example

File: hsfau.recoder

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments