maskfeat

maskfeat

maskfeat masks features of a sequence.

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]:

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 want to mask. See Chapter 2 for a list of the EMBL feature types, and Chapter 3 for a list of the SWISS-PROT feature types. The type may be wildcarded by using *. If you want to mask more than one type, separate their names with spaces or commas. For example:

 *UTR repeat*
-maskchar (string)

Character to use when masking. Default is X for protein sequences, and N for nucleic sequences.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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