EMBOSS: silent


Program silent

Function

Silent mutation restriction enzyme scan

Description

silent does a scan of a nucleic acid sequence for silent mutation restriction enzyme sites.

Usage

Here is a sample session with silent:

% silent
Silent mutation restriction enzyme scan
Input sequence: embl:hsfau
Comma separated enzyme list [all]: ecori,hindiii
Output file [hsfau.silent]: 

Command line arguments

   Mandatory qualifiers:
  [-seq]               sequence   Sequence USA
   -enzymes            string     Comma separated enzyme list
  [-outf]              outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -sshow              bool       Display untranslated sequence
   -tshow              bool       Display translated sequence
   -allmut             bool       Display all mutations


Mandatory qualifiers Allowed values Default
[-seq]
(Parameter 1)
Sequence USA Readable sequence Required
-enzymes Comma separated enzyme list Any string is accepted all
[-outf]
(Parameter 2)
Output file name Output file <sequence>.silent
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-sshow Display untranslated sequence Yes/No No
-tshow Display translated sequence Yes/No No
-allmut Display all mutations Yes/No No

Input file format

Nucleic acid sequence USA.

Output file format

This is the result of the example above:

Results for HSFAU:

KEY:
        Enzyme          Enzyme name
        RS-Pattern      Restriction enzyme recognition site pattern
        Match-Posn      Position of the first base of RS pattern in sequence
        AA              Amino acid. Original sequence(.)After mutation
        Base-Posn       Position of base to be mutated in sequence
        Mutation        The base mutation to perform

Silent mutations

Enzyme      RS-Pattern  Match-Posn   AA  Base-Posn Mutation
     



Results for reverse of HSFAU:

Silent mutations

Enzyme      RS-Pattern  Match-Posn   AA  Base-Posn Mutation
     
HindIII     AAGCTT         267       A.A    268      A->T  

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
chaosCreate a chaos game representation plot for a sequence
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
diffseqFind differences (SNPs) between nearly identical sequences
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
einvertedFinds DNA inverted repeats
equicktandemFinds tandem repeats
etandemLooks for tandem repeats in a nucleotide sequence
isochorePlots isochores in large DNA sequences
newcpgreportReport CpG rich areas
newcpgseekReports CpG rich regions
palindromeLooks for inverted repeats in a nucleotide sequence
polydotDisplays all-against-all dotplots of a set of sequences
rebaseextractExtract data from REBASE
redataSearch REBASE for enzyme name, references, suppliers etc
remapDisplay a sequence with restriction cut sites, translation etc
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
tfscanScans DNA sequences for transcription factors

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

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.

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