]> Mask off regions of a sequence. (EMBOSS) edit http://bioweb.pasteur.fr/docs/EMBOSS/maskseq.html maskseq &emboss_init; input Input section sequence sequence -- any [single sequence] (-sequence) perl " -sequence=$value -sformat=fasta" 1 any 8 seqfile perl 1 required Required section regions Regions to mask (eg: 4-57,78-94) (-regions) perl " -regions=$value" 2 Regions to mask. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are separated by any non-digit, non-alpha character. <BR> Examples of region specifications are: <BR> 24-45, 56-78 <BR> 1:45, 67=99;765..888 <BR> 1,5,8,10,23,45,57,99 tolower Change masked region to lower-case (-tolower) 0 perl ($value)? " -tolower" : "" 3 The region can be 'masked' by converting the sequence characters to lower-case, some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the '-supper' flag. maskchar Character to mask with (-maskchar) acd @($(acdprotein)?X:N) perl " -maskchar=$value" 4 Character to use when masking. <BR> Default is 'X' for protein sequences, 'N' for nucleic sequences. <BR> If the mask character is set to be the SPACE character or a null character, then the sequence is 'masked' by changing it to lower-case, just as with the '-lowercase' flag. output Output section outseq outseq (-outseq) outseq.out perl " -outseq=$value" 5 seqfile perl 1 outseq_sformat Output format for: outseq fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 6 auto perl " -auto -stdout" 7