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silent
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Find restriction sites to insert (mutate) with no translation change
Description
silent finds restriction enzyme sites in a nucleotide sequence which
can be inserted (mutated) without changing the translation. silent
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, insert 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, all
possible mutations are shown and the untranslated and translated
sequence are reported.
Usage
Here is a sample session with silent
% silent
Find restriction sites to insert (mutate) with no translation change
Input nucleotide sequence: tembl:x65923
Comma separated enzyme list [all]: ecori,hindiii
Output report [x65923.silent]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Find restriction sites to insert (mutate) with no translation change
Version: EMBOSS:6.4.0.0
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 [*.silent] 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
-allmut boolean [N] Display all mutations
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
-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
silent 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 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 sequence 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="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="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.silent
########################################
# Program: silent
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: silent
# -sequence tembl:x65923
# -enzymes ecori,hindiii
# Report_format: table
# Report_file: x65923.silent
########################################
#=======================================
#
# Sequence: X65923 from: 1 to: 518
# HitCount: 1
#
# 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
# Silent: Yes for unchanged amino acid
# Mutation: The base mutation to perform
#
# Creating silent and non-silent mutations
#
#=======================================
Start End Strand EnzymeName RS-Pattern Base-Posn AAs Silent Mutation
267 272 - HindIII AAGCTT 268 A.A Yes A->T
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_length: 518
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------
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
None.
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
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
restover Find restriction enzymes producing a specific overhang
restrict Report restriction enzyme cleavage sites in a nucleotide
sequence
showseq Displays sequences with features in pretty format
silent does the opposite to recode. silent finds sites where a
restriction enzyme site can be introduced without changing the
translation in frame 1 of the sequence. recode finds sites where a
restriction enzyme site can be removed without changing the translation
in frame 1 of the sequence.
Author(s)
Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Written (Aug 2000) - Alan Bleasby.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
