EMBOSS: maskseq


Program maskseq

Function

Mask off regions of a sequence

Description

This simple editing program allows you to mask off regions of a sequence with a specified letter.

Why would you wish to do this? It is common for database searches to mask out low-complexity or biased composition regions of a sequence so that spurious matches do not occur. It is just possible that you have a program that has reported such biased regions but which has not masked the sequence itself. In that case, you can use this program to do the masking.

You may find other uses for it.

Usage

To mask off bases 10 to 12 from a sequence 'gatta.seq' and write to the new sequence file 'gatta2.seq':
% maskseq gatta.seq gatta2.seq -reg=10-12 

To mask off bases 20 to 30 from a sequence 'hdh.seq' using the character 'n' and write to the new sequence file 'hdh2.seq':

% maskseq hdh.seq hdh2.seq -reg=20-30 -mask=n

To mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'yuy.seq':

% maskseq yuy.seq yuy2.seq -reg=20-23,34-45,88-90

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outseq]            seqout     Output sequence USA
   -regions            range      Regions to mask.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are separated by any non-digit,
                                  non-alpha character.
                                  Examples of region specifications are:
                                  24-45, 56-78
                                  1:45, 67=99;765..888
                                  1,5,8,10,23,45,57,99

   Optional qualifiers:
   -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 USA Readable sequence Required
[-outseq]
(Parameter 2)
Output sequence USA Writeable sequence <sequence>.format
-regions Regions to mask. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 Sequence range None
Optional qualifiers Allowed values Default
-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

This program reads in a single sequence file.

You can specifiy a file of ranges to mask out by giving the '-regions' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-regions @myfile').

The format of the range file is:

An example range file is:


# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

Output file format

Single sequence file.

Data files

Notes

This can be used as a simple sequence editor.

References

Warnings

You can mask out a complete sequence.

Diagnostic Error Messages

Several warning messages about malformed region specifications:

Exit status

It exits with status 0, unless a region is badly constructed.

Known bugs

Bugs noted but not yet fixed.

None.

See also

Program nameDescription
cutseqRemoves a specified section from a sequence
descseqAlter the name or description of a sequence
extractseqExtract regions from a sequence
maskfeatMask off features 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

Completed 3 March 1999

Target users

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

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