maskfeat

Function

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.

Some non-EMBOSS programs (for example FASTA) are capable of treating lower-case regions as if they are masked. maskfeat can mask a region to lower-case instead of replacing the sequence with 'N's or 'X's if you use the qualifier '-tolower' or use a space character as the masking character.

Usage

Command line arguments


Input file format

maskfeat 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

maskfeat writes out a normal, masked, sequence file.

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.

Author(s)

History

Target users

Comments