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EMBOSS: maskfeat |
% maskfeat
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outseq] seqout Output sequence USA Optional qualifiers: -type string By default any feature in the feature table with a type starting 'repeat' is masked. You can set this to be any feature type you wish to mask. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. The type may be wildcarded by using '*'. If you wish to mask more than one type, separate their names with spaces or commas, eg: *UTR repeat* -maskchar string Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
-type | By default any feature in the feature table with a type starting 'repeat' is masked. You can set this to be any feature type you wish to mask. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. The type may be wildcarded by using '*'. If you wish to mask more than one type, separate their names with spaces or commas, eg: *UTR repeat* | Any string is accepted | repeat* |
-maskchar | Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. | Any string is accepted | 'X' for protein, 'N' for nucleic |
Advanced qualifiers | Allowed values | Default | |
(none) |
Program name | Description |
---|---|
cutseq | Removes a specified section from a sequence |
descseq | Alter the name or description of a sequence |
extractseq | Extract regions from a sequence |
maskseq | Mask off regions of a sequence |
megamerger | Merge two large overlapping nucleic acid sequences |
merger | Merge two overlapping nucleic acid sequences |
newseq | Type in a short new sequence |
noreturn | Removes carriage return from ASCII files |
nthseq | Writes one sequence from a multiple set of sequences |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a sequence |
splitter | Split a sequence into (overlapping) smaller sequences |
trimseq | Trim ambiguous bits off the ends of sequences |
vectorstrip | Strips out DNA between a pair of vector sequences |