EMBOSS: maskfeat

| ## EMBOSS: maskfeat

# Program maskfeat

## Function

Mask off features of a sequence

## Description

maskfeat reads in a sequence with its associated features. The features can be found in the annotation of the sequence if it is in a format such as EMBL or SWISSPROT which includes features in the annotation, or they may be supplied explicitly in a GFF file by using the command-lin option '-gff filename'.

The feature table is then searched for features whose type matches the specified feature type to be masked. By default, the type is 'repeat*' (i.e. any type whose name starts with 'repeat'). You can specify the name of any other type of feature, or features that you wish to mask. If you wish to specify more than one type of feature, separate their names with spaces or commas. The names of the types of feature to be found may be wild-carded with asterisks '*' to find gruops of feature types sharing a common part of their names.

If you are unsure of the names of feature types in use, please consult 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.

If any features matching the specified names of feature types are found, then those regions of the sequence will be masked out by replacing that part of the sequence by masking characters. The default masking characters are 'X' for a protein sequence and 'N' for a nucleic acid sequence, although you can specify your own masking character, if required.

## Usage

Here is a sample session with maskfeat. It masks out a feature whose type is "repeat_region" from position 2331 to 2356:

    % maskfeat em:AB000360
    Mask off features of a sequence.
    Output sequence [ab000360.fasta]:

## 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)
       General qualifiers:
      -help                bool       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 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

It reads in a sequence USA. You can optionally specify a GFF feature file to use with the command-line option '-gff filename'.

## Output file format

A normal, masked, sequence file.

The output from the above example is:

    >AB000360 AB000360 Homo sapiens PIGC gene, complete cds.
    ggatccctgctgcagagggggtaacggtgtctggcttgccaagcaatatttgttgtggtc
    tatcatggaagaaataaagtcgggcaatatgaattttttttttctcaaatttgccggatg
    gctgtggtgtttctgactcttagttttctcattgtgaaaaaggaatgattatcttcttcg
    atcctctcaagagtttccttgttttgagtagattgatagctctttaaaggatgctaagct
    cagctaatggaagaagagtctagtttctttgaggctttgattttggttaaactatagagc
    tcatacctttctgtatggtgcagcttactattgtctttggattggtaacttaaaaaatac
    aaataacatgcctttgagaaccaataaaaactatggatattatccctataaatttacaca
    aatccagatataagcatgcaatgtgatatacctaagggatatgtgaaccactgagttaag
    aactgctttagagggagatacaatgtgagacacaggctttgggataagactttggtttga
    atcctggctctgctctgttaccttagggcaaagttacttaagcatcttgaatctcagctt
    ttttaccaaagcaggactaatactaacttacaaggtggtgaggattaagtgaaagaagat
    acataaggcacttagcacatagtaggtactcaataagcgatagctaacagatgtctatta
    ttattcaaggaattataattttcaaatctgaaatgcagttttaatgtcccataaggtgac
    taccacatacatttttctcagacttttagtaaactgagttgatttgactttatctcagta
    ctactcttgacctttcacaactttcgtaggttcacagtctctctttttctaggaacttgg
    ctgtgttgtcctgcctcagagacaaattcatctattgtaggcctagcccctgcctttgaa
    aacaaggaaaggttggtagaacatcaacacagcatggaatttccagggaggtctcatttc
    aaaacttcataaagaacaagaaccacctggacttctgtgagggcgatgattaaactggcc
    tgagtttgaatgaaaggataatgtatgctcaacctgtgactaacaccaaggaggtcaagt
    ggcagaaggtcttgtatgagcgacagccctttcctgataactatgtggaccggcgattcc
    tggaagagctccggaaaaacatccatgctcggaaataccaatattgggctgtggtatttg
    agtccagtgtggtgatccagcagctgtgcagtgtttgtgtttttgtggttatctggtggt
    atatggatgagggtcttctggccccccattggcttttagggactggcctggcttcttcac
    tgattgggtatgttttgtttgatctcattgatggaggtgaagggcggaagaagagtgggc
    agacccggtgggctgacctgaagagtgccctagtcttcattactttcacttatgggtttt
    caccagtgctgaagacccttacagagtctgtcagcactgacaccatctatgccatgtcag
    tcttcatgctgttaggccatctcatcttttttgactatggtgccaatgctgccattgtat
    ccagcacactatccttgaacatggccatctttgcttctgtatgcttggcatcacgtcttc
    cccggtccctgcatgccttcatcatggtgacatttgccattcagatttttgccctgtggc
    ccatgttgcagaagaaactaaaggcatgtactccccggagctatgtgggggtcacactgc
    tttttgcattttcagccgtgggaggcctactgtccattagtgctgtgggagccgtactct
    ttgcccttctgctgatgtctatctcatgtctgtgttcattctacctcattcgcttgcagc
    tttttaaagaaaacattcatgggccttgggatgaagctgaaatcaaggaagacttgtcca
    ggttcctcagttaaattaggacatccattacattattaaagcaagctgatagattagcct
    cctaactagtatagaacttaaagacagagttccattctggaagcagcatgtcattgtggt
    aagagaatagagatcaaaaccaaaaaaaatgaaccaaaggcttgggtggtgagggtgctt
    atcctttctgttattttgtagatgaaaaaactttctggggacctcttgaattacatgctg
    taacatatgaagtgatgtggtttctattaaaaaaataacacatccatcaagttgtctcat
    gatttttccataaacaggaggcagacagaggggcatgaagagtgaagtaaNNNNNNNNNN
    NNNNNNNNNNNNNNNNaaagtcacttctttctacccttttcaatgtgctaatgctctttt
    atttatctagggctcaaatcttagaacacagggtgctatgctcagttttgttgcccaaga
    tcacagaattggttacttaaccttgactcagagtttctaccttgttcttagggaagcata
    tcacaactaattgcaaagcagagtgtgatgtgtcacaataagcagaatgctagggggaat
    tc

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
coderet | Extract CDS, mRNA and translations from feature tables
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
showfeat | Show features of a sequence
splitter | Split a sequence into (overlapping) smaller sequences
swissparse | Retrieves sequences from swissprot using keyword search
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

maskseq simply masks a user-specified set of regions, without using annotated features.

## Author(s)

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

## History

Written (2000) - Gary Williams

## Target users

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

## Comments