EMBOSS: silent

Program silent

Function

Silent mutation RE scan

Description

Usage

Here is a sample session with silent:


% 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

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

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Program name	Description
chaos	Create a chaos game representation plot for a sequence
cpgplot	Plot CpG rich areas
cpgreport	Reports all CpG rich regions
diffseq	Find differences (SNPs) between nearly identical sequences
dotmatcher	Displays a thresholded dotplot of two sequences
dotpath	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	Displays a wordmatch dotplot of two sequences
einverted	Finds DNA inverted repeats
equicktandem	Finds tandem repeats
etandem	Looks for tandem repeats in a nucleotide sequence
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
palindrome	Looks for inverted repeats in a nucleotide sequence
polydot	Displays all-against-all dotplots of a set of sequences
rebaseextract	Extract data from REBASE
redata	Search REBASE for enzyme name, references, suppliers etc
remap	Display a sequence with restriction cut sites, translation etc
restrict	Finds restriction enzyme cleavage sites
showseq	Display a sequence with features, translation etc
tfscan	Scans DNA sequences for transcription factors

Author(s)

History

Written (date) - author.

Target users

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