MASKSEQ(1e) | EMBOSS Manual for Debian | MASKSEQ(1e) |
NAME¶
maskseq - Write a sequence with masked regionsSYNOPSIS¶
maskseq -sequence sequence -regions range [-tolower toggle] -maskchar string -outseq seqout
maskseq -help
DESCRIPTION¶
maskseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit" command group(s).OPTIONS¶
Input section¶
-sequence sequenceRequired section¶
-regions rangeRegions 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
Additional section¶
-tolower toggleThe region can be 'masked' by converting the sequence
characters to lower-case, some non-EMBOSS programs e.g. fasta can interpret
this as a masked region. The sequence is unchanged apart from the case change.
You might like to ensure that the whole sequence is in upper-case before
masking the specified regions to lower-case by using the '-supper' flag.
Default value: N
-maskchar string
Character to use when masking. Default is 'X' for protein
sequences, 'N' for nucleic sequences. If the mask character is set to be the
SPACE character or a null character, then the sequence is 'masked' by changing
it to lower-case, just as with the '-lowercase' flag. Default value:
@($(acdprotein)?X:N)
Output section¶
-outseq seqoutBUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).SEE ALSO¶
maskseq is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
05/11/2012 | EMBOSS 6.4.0 |