EMBOSS: maskfeat


Program maskfeat

Function

Mask off features of a sequence

Description

Usage

Here is a sample session with maskfeat.

% maskfeat

Command line arguments

   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)

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
cutseqRemoves a specified section from a sequence
descseqAlter the name or description of a sequence
extractseqExtract regions from a sequence
maskseqMask off regions of a sequence
megamergerMerge two large overlapping nucleic acid sequences
mergerMerge two overlapping nucleic acid sequences
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
splitterSplit a sequence into (overlapping) smaller sequences
trimseqTrim ambiguous bits off the ends of sequences
vectorstripStrips out DNA between a pair of vector sequences

Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

History

Target users

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

Comments