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

Here is a sample session with maskseq

Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq':


% maskseq ../../data/prot.fasta prot2.seq -reg=10-12 
Mask off regions of a sequence.

Go to the input files for this example
Go to the output files for this example

Example 2

Mask off bases 20 to 30 from a sequence 'prot.fasta' using the character 'x' and write to the new sequence file 'prot2.seq':


% maskseq ../../data/prot.fasta prot2.seq -reg=20-30 -mask=x 
Mask off regions of a sequence.

Go to the output files for this example

Example 3

Mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':


% maskseq ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 
Mask off regions of a sequence.

Go to the output files for this example

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   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
  [-outseq]            seqout     Output sequence USA

   Optional qualifiers:
   -maskchar           string     Character to use when masking.
                                  Default is 'X' for protein sequences, 'N'
                                  for nucleic sequences.

   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
-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
[-outseq]
(Parameter 2)
Output sequence USA Writeable sequence <sequence>.format
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

maskseq reads in a single sequence USA.

Input files for usage example

File: ../../data/prot.fasta

>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
ACDEFGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWY

You can specify 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

maskseq writes s single masked sequence file.

Output files for usage example

File: prot2.seq

>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY

Output files for usage example 2

File: prot2.seq

>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY

Output files for usage example 3

File: prot2.seq

>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY
ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY

Data files

None.

Notes

None.

References

None.

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

None.

See also

Program nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping the first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

maskfeat masks parts of the input sequence that are annotated features whose feature-names match the user-specified names.

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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