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