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recoder |
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'.
% recoder Remove restriction sites but maintain same translation 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
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-enzymes string [all] Comma separated enzyme list (Any
string is accepted)
[-outfile] report [*.recoder] Output report file name
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
-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
-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 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 dying program messages
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| -enzymes | Comma separated enzyme list | Any string is accepted | all |
| [-outfile] (Parameter 2) |
Output report file name | Report output file | <*>.recoder |
| 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 |
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="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
//
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########################################
# Program: recoder
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: recoder
# -sequence tembl:x65923
# -enzymes EcoRII
# Report_format: table
# Report_file: x65923.recoder
########################################
#=======================================
#
# Sequence: X65923 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->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
81 77 Rev EcoRII CCWGG 79 P.P T->G
81 77 Rev EcoRII CCWGG 79 P.P T->C
111 107 Rev EcoRII CCWGG 109 P.P T->G
111 107 Rev EcoRII CCWGG 109 P.P T->C
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->G
201 197 Rev EcoRII CCWGG 199 P.P A->C
252 248 Rev EcoRII CCWGG 250 P.P A->G
252 248 Rev EcoRII CCWGG 250 P.P A->C
297 293 Rev EcoRII CCWGG 295 P.P A->G
297 293 Rev EcoRII CCWGG 295 P.P A->C
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 34
#---------------------------------------
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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:
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:
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.
| 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 |
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.
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/